Revelations
by T L Kay
Summary: AU about John. Previously titled The Other Sheppard The sequel The Other City was incorporated into this story so that it's just one. More of a description inside. Chapter 22 is up!
1. The Other Sheppard

The team is informed that they are getting a new team member. Who it turns out to be is a shock to John, a blast from his past that he didn't expect to see again. (Was originally in the already established universe but i guess it's kinda become an AU cause of character developments this upcoming season)

This story was previously posted under the title "The Other Sheppard" I have changed the title as I have combined it with the sequel "The Other City" because i was told that breaking it up was confusing. I have also done some serious editing because I found that there were many inconsistencies. I would advise reading the first few chapters through again as the rest of is might be confusing if you don't know of the changes. I hope you all enjoy it, and if you don't too bad. ) I've worked really hard on this, and it's kinda my baby. I welcome reviews, but I would ask that you be considerate. Thanks, enjoy!

* * *

It was a normal day at Atlantis. Colonel Sheppard's team was scheduled to return shortly and Dr. Weir was waiting anxiously. She had a surprise for the team that she couldn't wait to give them. All of a sudden the gate activated and the shield went up. 

"It's Colonel Sheppard's IDC ma'am," someone said.

"Let them through," she said, wondering why they were back early.

They strolled through the gate, Rodney and John bickering as usual. "Well, maybe if you hadn't told them their religion was stupid, Rodney, they wouldn't have kicked us out," John was saying.

"I didn't tell them it was stupid, I merely pointed out the fallacies in their faith," Rodney shot back.

"Oh, big difference."

"Are they always like this?" came a voice from next to Elizabeth. She jumped; she had forgotten that he was standing there.

"Dr. Jackson," said McKay, turning away from Sheppard. "What brings you here?"

"Ah, I just got in on the Daedalus. I was escorting a friend."

"Oh, did we get new people, Elizabeth?"

"Yes. In fact that's why I was waiting for you. I'd like you to come with me to meet your new team member."

"I'm sorry, new team member?" said John. "Why do we need a new team member?"

"How about we discuss this on the way to the infirmary?" Elizabeth asked.

John nodded and the group headed away from the gate room. "Ok, so, why do we need someone new?"

"Well, as I'm sure you are all aware, none of you is exactly qualified to deal with anything archaeological. Not to mention the fact that between the four of you you only know a handful of Ancient."

"Ok, so what," said John. "This new guy is a specialist…"

"Girl," murmured Daniel.

"I'm sorry?"

"Your new team member is a woman, not a man."

"I meant guy in general. Anyway. I know nothing about her, what makes you think I'm going to let her on my team?"

"Excuse me?" said Elizabeth, part amused part angry.

"Elizabeth, he has a point," said Rodney. "You made Ronon jump through all kinds of hoops before you'd let him join…"

"I didn't mind."

Rodney continued as if he hadn't noticed the interruption. "Why are you so eager just to drop someone new into the mix?"

"I don't need any other reason other than that she is the close friend and protégée of Dr. Jackson."

"Ok, that doesn't change the fact that we know nothing about her." Rodney continued.

"She comes from a military family, she attended the Air Force Academy, but chose to pursue her doctorate rather than join the military. She got her PhD in archaeology and linguistics last year at the age of 27. She has been studying with Dr. Jackson for the past 5 years and is the foremost expert on Ancient next to Daniel himself. Isn't that right Daniel?"

"Yep. I was training her to be my replacement at the SGC when I came to Atlantis, but things have come up, so she's taking my place here instead."

"She's also a brilliant pilot, and she has the gene."

"The Ancestor gene?" Teyla asked.

"Yes, and she's got it very strong. Possibly stronger even than you John, and some interesting side effects to go with it."

"Wait, what does that mean?" asked McKay. "What side effects?"

"Well, for starters, increased brain capacity. The doctors at the SGC theorized that the stronger the gene the more Ancient traits you inherit as well. Who knows what else she can do."

Sheppard's team was quiet for a moment, and then Rodney piped up again. "Is that all?"

"What more do you want Rodney? I've told you pretty much all that you need to know about her."

"Oh, I don't know. How about a name?"

Elizabeth smiled. "Well, we're here now. Why don't you ask her yourself?"

They walked through the entrance to the infirmary and looked around. There were a few occupants in the beds, but the person they sought was the one being inspected by Dr. Keller.

"All right. You're good to go," she was saying.

The young woman hopped down from the bed and turned to the group. There was a look of shock on Sheppard's face, as well as on the woman's.

"Johnny?" she said in almost a whisper.

Before John could speak she had thrown herself at him, hugging him tightly. When she finally pulled away she was looking at him as if looking at a dead man, and she had tears in her eyes.

The others were all staring at them; Ronon, Teyla, and McKay in curiosity.

John ignored them, staring at the woman in front of him. "Katie, what the hell are you doing here?"

"Hasn't anybody told you? I'm joining your team."

"You're the person Elizabeth has been talking about?"

"One and the same."

"But I don't get it, why didn't you tell me you were coming?"

She frowned at him. "Tell you how? Johnny you practically dropped off the face of the earth after that Afghanistan stuff."

"Katie…"

"No. I understand why you did at first, but it's been what 5, 6 years? I think that's enough time to ignore your loved ones."

"Katie it wasn't like that. Paul…"

"I know all about it John, but I never took you for a pushover."

"Now that's not fair, he was…adamant."

Kate glared at him.

John opened his mouth to say something further, but Rodney got there ahead of him. "I'm sorry to interrupt what is most likely a beautiful reunion. I wouldn't know seeing as we have no idea who you are. Who are you?"

Kate looked at John. "You haven't told them? Why haven't you told them John? Or are you gonna blame this on Paul too?"

John looked uncomfortable. "It's complicated Katie. Why bring up something that's going to lead to questions that I'm uncomfortable answering?"

Rodney was looking more and more interested. "This should be good," he whispered.

"Oh, so that's how this is going to be?" Kate asked sharply.

"Katie, you know how it's been. You know I love you."

"This just keeps getting better and better," McKay whispered.

"Shut up McKay," John said. "Or I'll shut you up."

"Shutting up now."

"Look, it just never came up, ok Katie?"

Kate was looking daggers. "Maybe I'll just leave, if you don't want me here." She grabbed her jacket from off the bed and headed for the door.

"Katherine Marie Sheppard, you stop right there," he yelled after her.

Kate froze in the doorway; the others froze too, glancing from John to Kate. She turned around, a smile on her face.

"Well, that's one way to tell them. Maybe you should fill in the gaps, though, before—McKay is it?—before McKay's imagination runs away from him."

"Hey."

"Oh come on John, stop looking at me like I'm a child."

"Well maybe if you didn't act like one all the time…"

Kate sighed. She turned from John to the small crowd standing apart from them. She extended a hand. "Hello, I'm Kate Sheppard. I'm John's baby sister."


	2. Reunions

"Ok Katie, what are you really doing here?" John asked his sister back in his room. He had finally managed to shake off the last of his friends—meaning Rodney—out in the hallway. Elizabeth had gone off to speak with Dr. Jackson before he left, and Ronon and Teyla had their usual sparring match, but Rodney was impossible to get rid of. His curiosity was a problem sometimes.

"What am I _really_ doing here? There's no ulterior motive here John. I'm here because I want to be."

"Don't you have any idea how dangerous it is here?"

"Well, if it's not too dangerous for you…"

"Katie…"

"Don't start with me. I don't want to hear it. I'm not a child anymore; I can take care of myself. And you need me here."

John sighed. "Fine."

"Fine? You're just gonna let it drop?"

"Well, I don't really have a choice now do I?"

Kate laughed. "No, you don't."

John sighed again. "So, what's been going on in your life? How's mom?"

"Mom's good. She's still in love with Paul for no reason that I can see."

"Is Paul the reason you didn't join the Air Force?"

"Yeah. You know I was only going to because of you and dad, but Paul was just getting irritating. When that thing happened with you he lost it, said that you should have been court-martialed, that they had gone easy on you. Every day he would rail against you, it was just too much. Finally I just couldn't take it anymore. I blew up at him, told him that he could never hope to be half the soldier you are. I'm sure I said some other choice words to him and then I stormed away. I haven't really spoken to him since. I try to talk to mom as much as I can, but I just can't stand that guy."

John was laughing. "I would have loved to be there to see you yell at him."

"It was liberating."

"I bet. So, working at the SGC with Dr. Jackson, how long's that been going on?"

"Um…5 or so years now, but I didn't start working with Dr. Jackson until 3 years ago, when he started training me as his replacement. Although, I didn't know at the time that's what he was doing. But then he couldn't come here and I was already set up to have this kind of position, so here I am."

"I really am happy to see you Katie."

"I know. And if I were in your position I'd be worried too. I've read all about the Wraith, I don't ever want to see one, but I think that I can handle myself if I do."

"I'm sure you can."

Kate walked over to her brother and gave him another hug. "I'm really glad that you're here. I really missed you."

John laughed again and hugged her back.

"So," said Kate, stepping back, "can I get the tour, or do I have to ask McKay, who's probably standing outside the door?"

There was a shuffling sound from the other side of the door as Rodney ran away, and Sheppard laughed.

"I can show you around. And if you'd like you can have a go flying one of the puddle jumpers."

Kate's face lit up with glee. "I like flying things."

"Well then, after you."


	3. The First Mission

Sheppard's team welcomed Kate as if she had always been a part. Teyla was beyond thrilled to have another female on the team, even if she showed it in her usual stoic way. Kate had a very boyish sense of humor and hit it off with Ronon almost instantly; even Rodney liked her, though he hid it very well. All in all she integrated very nicely, much to the pleasure of John and Elizabeth.

A week after Kate joined SGA-1 Elizabeth called John into her office.

"I've decided that it's time you guys went on a mission. I'm sure you've been enjoying your down time, but I feel convinced that Kate has adjusted well and is ready to go on a mission."

John smiled. "I thought you'd never give us the go ahead. She's been bugging me like crazy to go on a mission."

"Well, now's her chance, you'll be heading to M5R-279."

"Didn't Lorne's team already go there?"

"Yes, but they detected some readings that should interest McKay, and there's an unknown form of writing in the cave that the readings are coming from."

"Well all right then, sounds like fun," he said with a hint of sarcasm.

She smiled at him. "I know it's not your kind of adventure, but I'm sure you'll find something to keep yourself occupied. Pick on Rodney, you always enjoy that."

"Oh, you know me so well."

* * *

Roughly thirty minutes later Sheppard's team was ready to go. Kate and John had gotten into an argument about weapons. Kate wanted a P-90 but John seemed to think it was unnecessary; naturally Kate assumed it was because she was his baby sister, and things got a little out of control. It took them 15 minutes to stop arguing in hushed tones, as if no one knew what they were doing.

"Have fun," Elizabeth said to them with a hint of amusement.

John looked grudgingly at his sister as she clipped her P-90 to her vest. He never won fights between the two of them, and this wasn't exactly how he wanted to start her first mission. He shrugged off his tension and stepped through the gate.

Kate walked up to the shimmering blue surface and touched it. It was an odd sensation, cool ant wet, and at the same time not. She took a deep breath and stepped forward into the unknown. It was the most amazing thing she had ever experienced. It felt like eternity was stretching out before her and she spent the rest of her days zipping around space, and then at the same time it was only seconds before she was stepping through the other side to a place that looked like it could fit anywhere in middle America. There were plenty of deciduous trees, shrubs, and grass that pretty green color that meant it got lots of rain.

John looked up as the gate closed behind Kate and she just stood there. "Was that your fist time?" he asked with a smile.

She nodded. "I—" she started but her voice faltered. She cleared her throat and started again. "I hadn't ever gotten a chance to go through when I got this assignment, then I came here on the Daedalus, which was an amazing experience all by itself, but this…"

"Yeah, it sometimes has that effect on people."

"You think?"

He laughed. "Come on, there's more fun to be had. Right Rodney?" he yelled to McKay, who was a ways ahead of them.

"The readings are coming from this direction," he said, and headed off to the right.

"See? He's so excited he can barely contain himself."

Kate laughed and walked off in the direction Rodney was heading. They followed the readings back a trail to the mountain range. Rodney was standing at the entrance to a cave when they caught up with him.

"Well, the energy readings are definitely coming from in there. They're very unusual also. They seem like Ancient energy outputs, but something's not right."

"Well, let's find out," said Kate, and she brushed past him and into the cave.

"Katie!" John ducked in after her. "God only knows what could have been in here, never just stroll into a place; you always have to look around."

"Oh please, John. If there was anything dangerous here Major Lorne's team would have told us."

"That doesn't mean that something couldn't have come in here since then."

She glared at him. "Fine, sorry. Can we work now?"

"Fine. You and McKay poke around, do your nerdy stuff. Ronon and I are going to look around. Teyla, keep an eye on them."

Teyla smiled slyly, but didn't say anything. John took one last look at his sister, then stepped out of the cave, mumbling under his breath.

Kate smiled, then turned back to the cave wall. It was truly intriguing. She recognized the writing as some form of Ancient, but there was something different about it. She moved along the wall, following the writing back to where it all seemed to flow out from. At the very back of the cave wall there was a section of very heavy writing. McKay had been circling the room the other way, following the readings and ended up in the same place.

"There's something here," they both said at the same time, then looked at each other.

"The readings are the strongest right here," said Rodney.

"That makes sense, these markings seem to indicate something of importance here, but it's difficult to decipher what it means. This writing is unlike any Ancient I've seen before. And yet, there's something strangely familiar about it."

"Like how the energy seems to be Ancient, and yet also seems not to be?"

She nodded. "I just can't figure out where…" she trailed off as her eyes fixed on a specific part of the writing.

"Dr. Sheppard?" Rodney said.

"…where I've seen this before." She gave a little laugh.

"What is it?"

"This isn't possible, it can't be possible," she whispered.

"What can't be possible?" Rodney asked, frustration seeping into his voice. He wasn't used to people other than himself being this cryptic.

Kate reached out her hand to touch the wall, and found nothing. Her hand went right through the wall with enough momentum to throw her off balance. She had enough time to grab Rodney's vest in an effort to steady herself before both of them fell through the wall into blackness.


	4. Discovering the Impossible

Kate's first thought was of the pain that she was in; the second was of the room she was in. She managed to haul herself into a sitting position and look around. She and Rodney were lying on the cold hard ground in a chamber that was filled with an eerie light, and no visible way of generating it. She shifted so that she was closer to Rodney and rolled him onto his back. She couldn't tell where they had come in from, but judging from the pain she was in, and the fact that Rodney was still unconscious, she was fairly certain they had fallen quite a ways.

"McKay," she said, shaking him a little. "Rodney, come on, wake up." She shook him a little harder and he grunted.

"Where are we?" he mumbled.

"Still trying to figure that one out," she said, helping him sit up.

"I remember falling through a cave wall, did that actually happen?"

She smiled. "Yeah, we fell through the wall; the question now is how do we get back out?"

She slowly stood up, then reached out her hand to help Rodney. She was just pulling him to his feet when her radio went off.

"McKay, Katie, come in," said John's voice.

She tapped her radio on. "John?"

"Oh thank God," he said. "We've been trying to get a hold of you for about 20 minutes."

She and Rodney exchanged a look. "I didn't realize we'd been out for that long."

"What happened?"

"Your sister decided it would be fun to see if she could break her neck on her first mission, not to mention mine," said Rodney.

Kate let go of Rodney and he stumbled. "Fine, be that way," she said to him. To her brother she said, "We found an entrance in the wall that we weren't expecting. It's right in the back of the cave."

There was a pause and then a rock came plummeting down from somewhere above them, nearly hitting them.

"Hey! What are you trying to do, kill us?" McKay said.

"Just checking."

"For what? We already know things can go through the wall."

"But can they go back?" Kate mumbled. She looked around on the ground for the stone that had landed near her feet. She found it and threw it up at the area she guessed they had come from. Some twenty feet or so above them the rock disappeared into the wall.

"Ow!" came John's voice over the radio.

Kate laughed. "That's what you get for chucking it at us in the first place."

"So," he said, a little irritated, "things can pass both ways, why don't you just step through?"

"Ah, if only it were that easy," said Rodney. "But when are our lives ever easy?"

"What Rodney is trying to say," she said exasperatedly, "is that the entrance is about twenty feet above us, there's no way we can get up there."

There was a pause.

"Ok, hang tight. We'll figure something out."

"Will do," said Kate, then tapped her radio off. "Well, what now?" she asked Rodney.

"What were you going to say before we fell through solid rock?"

"Hmm?"

"You were going to say where you had seen that writing before. Something that wasn't possible?" Rodney asked with a groan as he stood up straighter.

"Ah yes. Well, I think that the writing was a hybrid language."

"A hybrid? Of what?"

"Ancient…and Goa'uld."

Rodney looked dumbstruck. "You're kidding, right?"

She shook her head.

"But that's not possible, is it? There can't possibly be Goa'uld in Pegasus; we don't need any more enemies."

"I don't know what to tell you McKay, it just is."

She glanced around the chamber again and realized that the walls were covered with the same writing.

"Well, while we're down here I can at least try to figure out what some of this says." She moved over to an area of the wall that was beneath the entrance. "Maybe there's something here that can help us get out."

"I'm sorry; I'm still back on Goa'uld in this galaxy. How would they even have found it? And why would this writing be a mix of their language and Ancient?"

"I don't know, that's what I'm trying to figure out. Maybe you should be trying to find the source of the energy readings."

He looked at her confusedly.

She sighed. "You know, for a genius you're kinda dumb. You said the readings were the strongest behind the wall, well look around, we're behind the wall."

"Well excuse me for being a little preoccupied with the imminent threat of death," Rodney said shooting her a dirty look. When she didn't respond he sighed, bending down to pick up his amazingly undamaged tablet and marching off in search of the power source. They searched for their respective quarries for several minutes before either of them found anything. Rodney was just starting to make frustrated noises when Kate found what she had been looking for.

"McKay, come here."

He grumbled about being ordered around but he came. "What?"

"I found a way out."

"Really, how?"

"This part here," she indicated a patch of writing on the wall, "is like a lock. If you press the symbols in the right order I believe a way out will open up."

"Huh." Rodney looked down at his screen. "There are some readings coming from here, whatever it is obviously requires some energy output. Well, shall we give it a try?"

Kate nodded and reached out. "Here's hoping we don't fall through the wall this time."

Rodney gave her a dirty look, but she ignored him and concentrated on the symbols. She pressed them and then stepped back, but nothing happened.

"Nothing happened," said Rodney.

"I noticed," she retorted.

He opened his mouth to say something scathing when the ground began to rumble.

"Ok, something's happening now."

"You think?" she said, stepping away from the wall.

A staircase folded out of the wall leading up to the place where they had come through, which was now open. But that wasn't the only thing happening. Walls were going up all around the chamber, opening up more chambers and rooms, full of what was clearly Ancient technology.

"I guess we found the source of the readings," shouted Rodney over the rumbling, but Kate wasn't listening. A wall had come up opposite the staircase that revealed an interesting find.

"McKay," she said, poking his arm. "You might want to take a look at this."

He turned around and gasped.

"Hey!" came John's voice from up above. "You guys ok down there?"

"You should come down here Sheppard," said McKay.

"Way ahead of you." His voice was closer and they turned to see him descending the stairs, with Ronon and Teyla close behind. He stopped as his eyes fell on the chamber across from the stairs. "Is that what I think it is?"

"If you think it's an Ancient stasis chamber, then yes, that's what it is."

They moved closer to it, so that they could clearly see the man inside.

"So that's…"

"Most likely an Ancient," Rodney finished.

"Not necessarily," Kate said.

"What's that supposed to mean?" John asked.

But she didn't get a chance to answer before the question answered itself. The cover of the chamber slid open and the man opened his eyes, his yellow glowing eyes.

Sheppard didn't even flinch, in one fluid movement he pushed his sister away from the Goa'uld and raised his gun.

"John no!" she shouted.

The man in the chamber looked around at them and then his eyes rolled up and he fell forward. Kate ducked past her brother and caught him, easing him to the ground. She checked for a pulse before turning to look at John, who still had his weapon raised.

"John please, put your weapon down; he's not going to hurt us."

"He's a Goa'uld Katie; of course he'll hurt us."

She stood up, blocking the man from John. "First of all, he's unconscious." She reached out and pushed John's gun down. "Second of all, he has no means to hurt us. He has no hand device, no weapons, and he's probably thousands of thousands of years old. Don't you want to know why he's here? I know I do. I didn't think the Ancients and the Goa'uld coexisted."

"Fine," John conceded. "But I don't want anyone alone with him."

"Fine." She looked around and saw a shelf that looked like it could be used as a bed. "Could someone help me move him?"

They all looked at her.

"He's unconscious, it'll be ok."

John shrugged uncomfortably. "Fine, Ronon?"

The two of them picked up the unconscious Goa'uld and lifted him onto the shelf.

"All right, good. Now, I'm gonna have a look around at these machines, Dr. McKay will you assist me so that I know what I'm looking at?"

"What makes you think I'll know what they are?"

She shot him a look.

"Fine, I'm coming," he mumbled. "She's just like you," he shot at Sheppard. "And not in a good way."

John smiled in spite of himself as McKay trudged after Kate, but his humor was cut off when he looked back at the man next to him. This was going to end badly, he could just feel it. He had only ever dealt with a Goa'uld once, and it had almost destroyed Atlantis. He wasn't looking forward to what this one had up his sleeve, but he trusted his sister, so he was willing to wait and see.


	5. Sacrifices

It took about forty minutes for the man to regain consciousness and by then Kate and Rodney had found an information console and started translating it.

"His name is Adrianus," she said, scrolling through the screen. "This is truly fascinating. It seems he and several other Ancients composed a team of researchers looking into…something. This word is unfamiliar to me, but I think it was important. He and the others seemed to be on their way to Atlantis from…again an unfamiliar word, but they were attacked by the Wraith and their ship went down here. They set up shop here to continue their work while they waited for rescue."

"But rescue never came?"

"Doesn't look like it. And it looks like he's the only survivor. I'm guessing from what I can translate that he crashed here about the same time as the Lanteans were abandoning the Pegasus galaxy."

"I'd like to know what it was that was so important," said John.

The man behind him groaned and shifted. Kate darted over and got to his side before John could stop her. She helped him into a sitting position, despite John's protests. The man looked around in confusion.

"Hello, my name is Kate Sheppard, and you're Adrianus, aren't you?"

He took a wheezy breath. "I am, but you are not Alteran. Who are you?" He spoke in a non-echoing voice, albeit a strained and wheezy one.

"We're from Earth," she said.

Adrianus looked at her in amazement. "From Earth?"

"Yes, but we live in Atlantis."

This seemed to confuse him even more.

"About the time that you and the others crashed on this planet the Lanteans were evacuating the city, back to Earth."

"I was afraid they would do that. I tried so hard to make it in time, tried so hard…" he trailed off into a hacking cough. He coughed so hard he fell forward, but was caught by Kate, who eased him back onto the shelf.

"You should rest, you're not well."

"Silly girl," he said. "I'm dying. I was dying when I went into that thing, I only did it to make sure that someone would find me and I could pass on the information. How much time has passed since my people abandoned the city?"

John made a noise at the phrase "my people" but Kate silenced him with a look. She turned back to Adrianus with a sad look. "Nearly 10,000 years," she said.

He sighed. "Then it was all for nothing. The Wraith won."

"No they didn't," said John; he couldn't help himself; "we're still fighting them. If you have anything that could help us that would be great."

Adrianus coughed again, worse than before. "There's so much to say and so little time. I fear that this body will not last that long."

John gave him a dirty look, which he didn't see.

"Are you saying that…I'm sorry, I don't really know whether I'm talking to the host or the symbiote?" asked Kate.

He smiled. "A valid question. You are speaking now to the…symbiote you called me?"

She nodded.

"I am afraid that the host slipped into a coma some time before I entered the chamber."

"Well, how much time do you think you have?"

He looked her in the eye.

"That bad huh?"

He nodded.

Kate thought very quickly. She knew what she had to do, but that didn't mean that she necessarily wanted to do it, and she would only get one shot.

"Hey John," she said, turning to him. "Could you grab me that water over there?" The water was close enough that John wouldn't be leaving them alone, but far enough away that he might not get there in time if Adrianus decided to try anything. "It'll be fine John, I promise."

John gave her a questioning look, but obliged. As soon as he started walking away Kate acted. She leaned up to Adrianus and kissed him, or so it seemed.

"Sheppard!" Ronon yelled.

John turned to see his sister locked at the face to the Goa'uld.

"Katie!" he yelled, pulling up his gun, but he was too late.

Kate fell back from Adrianus and the man crumpled, lifeless. There was blood dripping from her mouth.

"No, dammit!" Sheppard yelled, racing to her side.

"Sorry John," she mumbled before her eyes flashed and she passed out.


	6. Near Miss

John burst through the gate at a run with Kate in his arms.

"John, what's going on?" Elizabeth asked, coming down the steps to meet them.

John ignored her and, placing his sister gently on the waiting stretcher, issued a series of commands to the medic. "Set up a level 3 quarantine, with armed guards at the door. Tell Dr. Keller that roughly 20 minutes ago a Goa'uld parasite took her over."

"What!?" interjected Elizabeth, but John kept going.

"A few minutes later her heart rate slowed and her breathing became shallow. Got that?"

They nodded.

"Then go."

"John, what the hell is going on?" Elizabeth asked as soon as the medics had left.

"We found a secret Ancient research chamber. There was an Ancient there, who happened to be a Goa'uld host."

"What? How is that possible?"

"I don't know. I wanted to kill him right at the start, but Katie wouldn't let me. She seemed to think he was good."

"But clearly he wasn't if he took your sister as a host."

John gave a cold, emotionless laugh. "No, she did this to herself."

Elizabeth looked astonished.

"The man was dying and didn't have time to tell us what he wanted to tell us. So she tricked me. She got me to move away, then allowed herself to be taken over."

"But why would she do that?"

"I told you, she believes he's good, and that he has valuable information that we couldn't pass up."

"This is bad John. The last time we had a Goa'uld in the city…"

"I know. But I didn't know what to do."

"It's ok, I understand. Go on, I'll get more information out of Rodney."

John gave her a questioning look. "You sure?"

She nodded. "Go see to Katie."

He gave her a grateful look and then raced after the medics. He got to the infirmary as they were transferring her from the gurney to a bed; Keller was issuing commands. As John walked through the door a flat beep met his ears.

"Katie!" he yelled, lunging forward.

"Get him out of here!" Keller shouted as she wheeled in the crash cart.

The marines stepped forward and attempted to bustle him out of the infirmary, but he ducked them and ran back into the room.

"Clear!" Keller said, before giving Kate a jolt from the paddles. "I said get him out of here!" For John had made another move for his sister.

He suddenly felt huge arms around him and twisted to see Ronon pulling him out of the room. He tried to get away but was no match for the bigger man. Ronon set John down outside the infirmary, but stayed close enough to him to prevent him from going anywhere. John thought for a moment before pulling out his firearm and pointing it at his friend.

"I will shoot you Ronon."

"Good thing we're next to the infirmary."

"Damn it!" John said, pointing his gun a little closer. "Don't make me do it."

"Let the doctor's do their jobs, Sheppard. They can't save your sister with you interfering.

John's finger was just inching toward the trigger when Dr. Keller stepped into the hallway. He took a step toward her and faltered. He didn't know if he wanted to know what she had to say.

"She's fine," said Keller.

John sagged, catching the wall for support and easing himself onto the ground.

"We've stabilized her, but we were unable to remove the symbiote, not without killing her."

"So what does that mean?"

She shook her head. "I don't know. I guess we'll have to wait until she wakes up. Which could be anytime."

"Can I see her?"

Keller nodded. "She probably won't know you're there, but you can go ahead."

John nodded and got up off the floor. "Thank you," he said.

"No need to thank me, Colonel, it's my job."

He nodded again, then went into the infirmary. Ronon made to follow him, but Dr. Keller stopped him.

"She's not out of the woods yet," she said. "And if the time comes that her condition declines, I'm going to need you to keep him out of the way. Can you do that?"

Ronon nodded. "Do you really think that'll be necessary?"

She glanced into the room, taking in Sheppard sitting by his sister's side, holding her hand. Keller nodded. "Yes, I really do."


	7. Consequences

After that John never left the infirmary; he wasn't going to leave his sister's side until he knew she was ok. Ronon kept him company, and although John knew the real reason his friend was there, he didn't care. Elizabeth postponed their missions, not only because of Kate and John, but to give Rodney the time to collect the immense amounts of data from Adrainus' lab. When the rest of his team wasn't off world they came by the infirmary, so John was never alone. One day, almost a week after the Goa'uld took Kate over and when Ronon was out, Major Lorne dropped by.

"Hello Major," said John as he got up from his seat next to Kate's bed.

"Colonel." Lorne looked uncomfortable. "Just came by to see how she's doing…how you're doing sir."

John restlessly ran his fingers through his hair. "There hasn't been any change. Thankfully she hasn't gotten worse, but she also hasn't gotten better."

Lorne nodded. John noted the concern on the Major's face.

"Did you get a chance to meet my sister, Major?"

Lorne shifted. "Not here sir, no. But I met Kate back at the SGC when we were both working there. She was, I mean is a good friend, sir."

John smiled. Lorne was a good person, a good soldier, he was glad that Kate had befriended him. "Well, I'll make sure you know if there's any change."

"Thank you sir." He looked like he was going to say more, then seemed to think better of it. He nodded then left, nearly bumping into Ronon, who was just entering.

"Hello Ronon," said John, turning his back on the man and taking his seat. "I was beginning to think you weren't coming."

Ronon stepped into John's line of vision and sank into the chair opposite him. "I wouldn't miss it."

John couldn't help but smile. He knew Ronon was there to babysit him, but he was getting to enjoy the man's company.

"So what kept you?"

Ronon shrugged. "McKay couldn't be dragged away from that place."

John nodded. "Well, when Rodney gets attached to something…but why did you go? I thought Lorne was in charge of that."

"He asked Dr. Weir for some time, so I went instead. That place gives me the creeps Sheppard. Thinking about having a snake in my head…" he broke off and shuddered slightly, which for him was unusual.

"Well, there was only one that we know of, so I don't think you have to worry."

"I didn't say I was worried."

John smiled again. "Of course not."

They sat for several moments in silence, just taking everything in. This was normal for them, a distinct lack of conversation, and yet John couldn't help but feel awkward this time. He shifted in his chair and opened his mouth to speak when he was interrupted by Elizabeth's entrance.

"Hello John," she said. "How are you doing?"

He shrugged as he got to his feet.

"Do you feel up to a quick walk?"

He glanced anxiously down at Kate.

"We won't go far," she said with a smile.

John nodded and followed her out into the hallway. "What's up?" he asked, assuming it had something to do with his team.

"It occurred to me that you've never talked about your sister, and I wondered why that was. And then, with this happening, you must want to talk."

John didn't know what to say. He felt an intense urge to hug her, but felt that would only lead to awkwardness. Instead, he cleared his throat and began to talk.

"I was almost eleven when Katie was born. Naturally I wasn't too pleased. My mother was a nurse with the Air Force, my father a General, so most of Katie's care fell on me; they hated the idea of us being raised by a nanny, so I got the job. Then, when she was two our father died. It was rough; my mom had to work extra long hours and more than ever before I became Katie's guardian. I took care of her for ten ears, almost more of a father than a brother. I put off going to college so that I could take care of them. And then, almost out of nowhere my mother was in love and getting married. Paul's things were barely moved in before he shipped me off to the Academy. He rarely let me come home, I was a disappointment. He said I lacked initiative, and he didn't like the choices I made in my personal life." He grimaced, but continued before Elizabeth could probe any further. He didn't like talking about his ex-wife.

"Then there was that whole thing in Afghanistan. After that I was completely cut off. Paul wouldn't let me anywhere near my sister, wouldn't let me see her, talk to her. It was horrible. That was the main reason I chose to be stationed in Antarctica. If I couldn't see the most important person in my life, then I really didn't care anymore.

"Nonetheless it was hard to take this assignment. The middle of nowhere on Earth was one thing, the middle of nowhere in another galaxy…But in the end, when Paul stonewalled me again I decided to come here. Katie was doing well at the Academy; she didn't need my black mark hindering her."

"Is that how she felt?" asked Elizabeth. She had remained quiet for all of John's speech, but she could tell that he wasn't going to continue without some prodding.

"I wouldn't know, I couldn't talk to her," he said sarcastically.

"My point John is that your sister probably didn't feel the same way as your step-father. In fact, I'm certain she didn't. I had a chance to talk to her, before this unfortunate ordeal, and she told me her side of the story. Trust me; she doesn't hold anything against you."

"I should have been there for her despite Paul's objections. I should have been the family she needed, but I guess I was too scared that after all that she didn't want me to be, didn't need me to be."

To John's surprise, Elizabeth hugged him. "She needs you now," she said, pulling away. "Whatever your problem's in the past she's here now and you can start over."

They had made a small circuit around the hall and were now standing back outside the infirmary. They walked through the door and John stopped dead at the sight that met him. Dr. Keller and her team were gathered around Kate's bed and Ronon was standing off to the side. John's heart seemed to have leapt into his throat, but then he heard the familiar "beep beep" of the heart monitor. It calmed him down, even if it was a slower beep than before.

He stepped forward but Ronon stopped him from going any further. He didn't say anything he just gave John a look, and with a sigh John complied. They stood there for several moments as Dr. Keller issued commands in a concerned voice. And then it happened.

"Beeeeeeeeeeeep."

John's heart seemed to stop with his sister's. He lunged forward, knowing that Ronon would stop him, but having to try. If John had been at all lucid he would have noticed that Ronon wasn't bustling him out of the room, just holding him there. John fought with everything he had to get away from the bigger man, but it was no use.

To John it seemed that the whole world slowed down, and all he could hear was that cold, flat beep. If it would just go back to the way it was everything would be ok, the world would be right again.

Elizabeth watched the scene with tears welling up in her eyes. She prayed that Kate would come back, come back for John's sake, because she didn't think that the man could survive getting her back just to lose her.

Dr. Keller paused in her attempts to resuscitate Kate and looked at the clock. With a sigh she switched off the monitor. "Time of death, 3:14 pm," she said.

A sound unlike any Elizabeth had every heard from her second-in-command escaped him and he fell to the floor, Ronon letting go of him. She sank down next to him and pulled him into her arms, letting him sob into her shoulder.

They heard a gasp and looked up to see Kate sitting bolt upright in the bed, breathing heavily and looking around in confusion.

"Katie?" John asked in astonishment, not able to move from his position on the floor.

"Johnny?" she said, before her eyes rolled back in her head and she collapsed back onto her pillows.

John moved lightning fast, getting to her side right as Keller switched on the heart monitor to reveal the steady "beep beep" of normal heart rhythm. John took his sister's hand in his and bent over her, shaking from silent sobs.

"What just happened?" Ronon asked as Elizabeth got to her feet.

"I could be mistaken, but I think the Goa'uld just sacrificed itself for her."

Ronon looked at her in surprise. "I thought those things were evil, why would it do that?"

"That," she sighed, "is an excellent question."


	8. The Other City

John made sure his sister was sleeping comfortably before stepping into the other room with Elizabeth and Dr. Keller.

"Someone wanna tell me what just happened in there?"

"I don't know Colonel," said Dr. Keller. "But the symbiote is gone. I can only guess that it sacrificed itself to save her."

"They can do that?"

Elizabeth nodded. "Yes. A similar thing happened to Col. Carter several years ago."

"Really?" he asked, stunned.

"Yes. You do know about the Tok'ra, right?"

"Well, yeah. Are you saying that you think this one, Adrianus, was a Tok'ra?"

"I believe that this one probably predated the Tok'ra, but it's possible that he also predated the kind of Goa'uld that we know now."

"Sheppard!" yelled Ronon from the other room.

John and the two doctors entered to find Kate struggling with Ronon to get out of the infirmary, and she was putting up quite a fight.

"Let her go, Ronon," he ordered.

The other man looked at him bemused.

"I want to know where she needs to get to so desperately. We can follow her," he added, grabbing a Wraith stunner from one of the nearby marines.

Ronon shrugged, but complied, and Kate immediately took off. John and Ronon exchanged a look before trailing after her. She headed straight to Rodney's lab, where he was sitting mulling over the data from Adrianus' lab.

"Hey!" Rodney shouted as Kate brushed him out of the way and grabbed his lap top. He grabbed hold of it, and engaged in a childish tug-of-war with her.

"Rodney!" came a disapproving voice from behind them. John turned to see that Elizabeth had followed. "Give her the laptop."

"But it's mine," he whined.

Elizabeth just glared at him over her crossed arms.

"Fine," Rodney said huffily, letting go of the laptop.

Kate tucked it under her arm and grabbed several data disks from the table.

"Elizabeth…" McKay started.

"Rodney, don't start with me."

Rodney grumbled under his breath, but didn't say anything else.

Kate glanced around the lab again, checking to see if she needed anything, then turned and left. She led them through countless corridors, down numerous stairwells, and used several transporters. When she finally halted, they were in a part of the city far far away from the control tower, a part that they hadn't even begun to explore yet. Kate looked around before entering a lab. Once inside she went straight to one of the consoles, turning it on and hooking up the laptop.

"Katie?" said John warily, inching toward her.

"I'm not crazy John," she said without looking up.

He sighed in relief. "Well you're sure acting like it. Why didn't you just ask Rodney for his laptop?"

Kate looked back at them with a sly smile. "I knew he'd never give it to me if I asked nicely."

"Hey," said Rodney as John laughed.

"I needed it, and I didn't really want to argue with him," she said turning back to console.

"What exactly are you looking for?"

"That," she said with satisfaction as she brought up a diagram of a galaxy.

"That's not this galaxy," said Rodney, stepping forward, intrigued.

"No, and it's not the Milky Way," she said.

"It's…Andromeda?" Rodney asked.

Kate nodded, turning back to the console and fiddling with it so that the image zoomed in on a specific solar system and a specific planet.

"What's that?" asked Rodney as gate symbols appeared.

"That," she said with a smile, turning back to them, "is the location of Praesidium, the _other_ lost city of the Ancients."


	9. Homecomings

The gate shut down behind the small group from Atlantis and General Landry stepped forward to greet them.

"Colonel Sheppard, Dr's Weir, McKay, Sheppard, welcome home."

"Thank you General," said Elizabeth, stepping forward. "It was nice of you to allow us to return ahead of schedule."

Landry laughed. "Well, this is something we are very eager to investigate. You are welcome to settle in after your visit to the infirmary. You won't be briefing us until tomorrow as Dr. Jackson is not back yet, and he practically begged us to wait for him."

Kate smirked at the thought of what her mentor's reaction must have been when he heard there was a second Lost City. Her amusement was cut short when Landry looked at her. Though he didn't say anything she knew that he considered her a safety risk. She stepped forward with a sigh.

"Good to see you again sir," she started off politely. "You don't need to say anything. I'm sure there's a nice secure room for me to go to where the medical people will meet me and where I'll be constantly supervised by highly trained marines?"

Landry shifted uncomfortably. "I'm afraid so Dr. Sheppard. You understand…"

"Of course I do, really it's ok." She stepped forward to meet the marines standing behind him. "Lead the way boys."

"Sir was that really necessary?" asked John after she had left.

"Yes it was. She had a completely unknown foreign entity residing in her. We just can't risk it until we're absolutely sure. We have a representative from the Tok'ra coming to give us their opinion. Once we're absolutely sure she's clean we'll let her loose. She understands son, I'd like it if you would too."

John sighed. "Yes sir."

"Now, if you'll excuse me, I have a meeting I must attend to. You three remember where the infirmary is?"

* * *

"Hey there," said a voice from the doorway. John looked up to see Sam standing there smiling down at him. He quickly noted the diamond sparkling on her finger before standing up.

"Colonel Carter," he started, but she cut him off.

"John, please. All that time on Atlantis together I think we know each other well enough to use first names."

He smiled. "Sam. How are you?"

"Good, enjoying being back on Earth. I mean, don't get me wrong, I loved Atlantis, but there's nothing like good ol' Earth. How about you?"

He shifted uneasily.

"I'm sorry, that's a dumb question. This can't be easy for you."

"It's fine now, well I shouldn't say fine, but it was the past two weeks that were hard. First there was that whole week where I didn't know if my sister would ever wake up again, then this past week she's been so disconnected, I can't reach her."

"Maybe I should talk to her."

"Did you know her well when she was here?"

Sam shrugged. "Not well really. I mean I saw her around a lot, and she was often with Daniel, but I know first hand what she's going through. When Jolinar sacrificed herself for me and then I was left with all those memories, it was hard. Even harder for the fact that I didn't have someone to help me through it who had been in my shoes. I'd really like to see if I can help Kate."

John nodded. "That would be wonderful; god knows she won't talk to me. There was that first day, just after she came back, where she was racing around finding all this stuff and talking nonstop, then she was all quiet and reserved. She's never really been a talker, but she's never really been quiet either, you know?"

"I understand. Don't worry, I'll talk to her." She turned to leave, but stopped, looking back over her shoulder. "And John? It's good to see you again."

"You too."

* * *

"Dr. Sheppard?"

Kate looked up from her lunch—which was being supervised by two marines—to find Colonel Carter smiling down at her.

"Col. Carter, how nice to see you again. Please sit down."

Sam smiled as she sank into the chair opposite. "How are you doing?"

Kate shrugged. "I'm not really digging the entourage," she said, nodding her head toward the marines.

Sam nodded. "Yeah, that's never fun. At least you're not locked up."

"Col. Carter, I know why you're here and I appreciate what you're trying to do, but I swear I'm fine."

Sam looked at her curiously. "Really?"

Kate nodded. "I know that you just want to help, but the circumstances are different. I knew what I was doing, what I was risking, but had to do it anyway."

"Your brother is very worried about you," Sam said.

"He's always worried about me," Kate said with a smile. "I'm really ok. I just needed some time alone with my thoughts, you can understand that."

Sam smiled weakly. "Yeah, I understand."

Kate sighed. "Well, thank you for the good intentions Col. Carter. I should get going now, I have to meet Dr. Lam so she and her team of medics can poke and prod me some more."

Sam laughed. "All right. It'll be fine, I'm confident that you're not evil."

Thanks," she said, standing up.

"And Kate?"

Kate turned back, surprised by the use of her first name. "Yes?"

"Talk to your brother."


	10. The Ancients

Kate sat in the briefing room after being cleared by the doctors. She looked around at the others settling in. There were her fellow Atlanteans, Elizabeth, Rodney, John; and then there was SG-1, including Jack O'Neill, who had been retired for several months. When they had all settled in they turned to Kate. She was slightly uncomfortable, she had no idea how much SG-1 knew about what had happened on M5R-279. She took a deep breath and leaned forward.

"I'll try and make this as short and to the point as possible, so I'll just get down to it. When the Alterans left this galaxy we originally assumed they all went to Pegasus, but this is not the case. There was a division among the Ancients about where to go. Many wanted to explore the Pegasus galaxy, but as many wanted to explore Andromeda, so they separated. As many Ancients as went in Atlantis took their other city, the space station Praesidium, and went to Andromeda. After the war with the Wraith started Praesidium became a kind of haven. Many scientists worked there to try and develop a weapon. Adrianus and his crew were on their way from Andromeda to Atlantis when their ship was struck down. They were carrying a message, that unfortunately was damaged in the crash. But it's likely that any useful information about the Wraith would still be there."

Daniel leaned forward, intrigued. "What can you tell us about the Goa'uld?"

Kate sighed, digging into the memories in her head that weren't hers. "Adrianus was one of several Ancients who returned to this galaxy thousands of years before the others. They were interested to see how life had evolved since they had left. During one of his adventures Adrianus discovered the Goa'uld home world. This was well before they had begun to take hosts, in fact," she paused, a little unsure about revealing the next little detail. She took a deep breath. "It's their fault," she finally said.

"What was whose fault?" asked Jack.

"The knowledge of blending, it's the Ancients' fault."

"Did they _ever_ think before they did stuff?" asked Jack.

Kate smiled weakly.

"So what happened?" Daniel asked, trying to steer the conversation back.

"Adrianus discovered a way to communicate with the Goa'uld and learned what his potential could be if he blended with one, so he did. The symbiote he took wasn't evil, nor was it necessarily good. It gained its sense of moral code from Adrianus."

"That's fascinating," started Daniel.

"Not really," said Jack. "So this Ancient dude willingly put a snake in his head and then, what, went back to Andromeda?"

"Yes. He hoped that together they could find a way to defeat the Wraith."

"And did they?"

"We have to go there to find out."

"You don't know? Shouldn't you have all of his memories?" Jack asked skeptically.

Kate shrugged. "I haven't gotten everything at once. And I don't get to pick and choose what I remember. I'm hoping that going to Praesidium will trigger more memories."

"Then that's what we're going to do," said General Landry.

"What?" said Jack.

"I already discussed this with the President and with the IOA. It was their decision that if the information was credible we should begin to plan an expedition."

"But Hank," said Jack. "Are we really sure this info is credible? No offense Dr. Sheppard."

"None taken," said Kate. "All I can say to that is that you have to trust me. From all your experience with the Goa'uld you have to know that I _know_ he was good."

"Jack she's right," said Sam. "There's no way the symbiote would be able to hide if from her if he was evil."

"Why not, they've been able to hide stuff from their hosts before, just look at Jolinar."

"But not whether they're good or evil. That can't be hidden."

"Oh all right," said Jack, giving in. "So, any thought to who's going on this crazy adventure?"

"Well, the IOA did have some suggestions but in the end the decision is mine and the President's."

"And?" asked Daniel.

"You're not going Dr. Jackson." Daniel's face fell. "Neither are you Dr. McKay," Landry added at the look on Rodney's face. "I think it would be best if we took a break. I need to talk to the President again, then we'll see about assigning this mission."


	11. Arrangements

"Dr. Jackson!"

Daniel turned to see Colonel Sheppard hurrying down the hallway to catch him.

"What can I do for you Colonel?"

"You have a lot of weight around here; you could affect a decision about who goes on this mission."

Daniel thought he knew where this was going.

"I want you to make sure Katie's on this mission."

Daniel was taken aback, that wasn't what he had been expecting. "I'm sorry, but I would have thought you'd be doing everything you could to keep her _off_ the mission."

"I know that it's going to be dangerous, but she deserves this. She risked everything to find this information; she should be the one who gets to discover this."

Daniel shifted uncomfortably. "I know, but that's not always how it works."

"But isn't that how it _should_ work? Think about how you felt when you weren't allowed to go to Atlantis. You know Katie well; you know what not getting this would do to her."

Daniel sighed. "I'll give it a try, but I can't guarantee anything."

* * *

"You wanted to see me sir?" Kate asked, standing just outside Landry's door.

"Yes Dr. Sheppard, please come in. Thank you Walter," he said to the man standing next to him, indicating that they were done.

"How are you doing after your…experience?" Landry asked after Sgt. Harriman had left.

Kate smiled softly. "Sir, I appreciate what you're trying to do, but I've never been one for small talk."

Landry laughed. "I can understand that. Well all right then, I'll get right down to it. We want you on this mission; in fact we would like to give you a command."

"Really?"

Landry nodded.

"Even though I'm not military?"

Landry smiled. "We had to pull some strings to get the IOA to agree, but eventually they did, with some exceptions. You will be in command of the first string team as long as you have a second in command of sufficient military ranking."

"Sufficient ranking?"

He sighed. "At least a Major. The IOA is uncomfortable with a lesser rank being in charge."

Kate smiled. "You would think they would have a problem with a civilian being in charge."

Landry smiled. "Yes, well, anyway, you will also be second in charge and take command should anything happen to the commanding officer. We're also prepared to let you choose your own team. I'll give you some time to think about it before you make a decision."

"I don't need any time, I already know."

"Really?"

"I want Major Lorne and Dr. Zelenka from Atlantis."

"I don't know if that's going to be possible…"

"I know Major Lorne well and we work well together, I trust him and can't think of anyone better for my second. And as for Dr. Zelenka, he's the foremost scientist in all things Ancient next to Dr. McKay, and since I can't have him…"

"Oh all right. I'll talk to Dr. Weir and Col. Sheppard. Anyone else?"

"Yes, a Captain Martin James. We were at the Academy together. He should be stationed in Afghanistan I believe."

"So he doesn't already have security clearance."

"No, sir, but there's no one I trust more."

"All right, I'll see what I can do. You can go now."

"Thank you sir, and if I might ask, who exactly is in charge?"

"General O'Neill."

* * *

"Damn it Jack, what the hell were you thinking? Did you have a brain aneurism or something?"

They were back at home and Sam was not happy. Jack had chosen to break the news at dinner in front of their son, hoping that Sam would remain calm. But Sam had nicely asked Jacob to go study before turning and blowing up at her fiancé.

"Sam please, it was the only way the IOA would sign off on this, and it's only temporary."

"You said you were done. We're trying to start a family here, Jack. What if you can't get back?"

"The Apollo will be standing by to retrieve us."

Sam scoffed, getting up from the table and going over to the window.

"Hey," said Jack, getting up and going over to her. He wrapped his arms around her waist and she sank into his embrace. "It'll be ok, I promise. You know me, I don't like adventure."

Sam laughed.

"I'm just going to make the stiffs at the IOA happy. I'll be back before you know it."

"You better," she said, turning around to face him. "You've got ten years to make up for."


	12. Old Friends

Rodney stood in the gate room watching the personnel from Atlantis who were going on the Andromeda expedition come through. He was trying very hard to contain his jealousy, but it wasn't very easy. He _really_ wanted to go on this mission, to the point that he was no longer allowed near General Landry from pestering him so much. He plastered a fake smile on his face and stepped forward to greet his friend.

"Hello Rodney," said Zelenka with a smug smile.

Rodney frowned. "You're enjoying this, aren't you Radek?"

Zelenka nodded. "A little bit. Oh come Rodney, you always get a chance to shine, now it's my chance. I'm sure they all wish that you could go, but then you wouldn't be at Atlantis and then where would we be? What you need to do is clone yourself, then you could go both places."

"But that wouldn't solve anything, because then my clone would be getting to have all the fun and we'd be back where we started."

"That was a joke, doctor," said a voice from behind them. They turned to see Major Lorne coming down the ramp as the gate shut down. "We'll all miss you McKay, but I'm sure we could send you a postcard or something."

Zelenka laughed.

Rodney opened his mouth to say something scathing but was cut off by John and Kate's entrance.

"Rodney play nice," said John. "We all wish you were going on this mission."

"We do?" whispered Zelenka to Kate.

John shot them a warning look. "Dr. Lam is waiting for you all in the infirmary. You know the drill; once you've been cleared you can do what you want. And Rodney," he added, grabbing the man's arm as he turned to leave with Zelenka. "Play nice."

"Don't I always?"

John laughed.

"I'll walk with you," said Kate to Major Lorne. "See you later John."

John nodded.

"Colonel," said Lorne, before turning and following Kate out. "So I really didn't get a chance to talk to you back on Atlantis, what with that whole dying thing."

She smiled. "Yeah, that was a bit inconvenient. "

"Yes. But I take it you've been well?"

She nodded. "As well as could be expected, with not knowing where my brother was and what he was doing." Suddenly she stopped, looking at him with a very serious expression. "Why didn't you tell me, Evan? I mean, it's not like we haven't talked over the past few years."

"Kat, I didn't know."

She looked at him skeptically.

"Sheppard is a pretty common name. He never said anything, and I never got enough out of you to make the connection. I swear I didn't know."

Kate smiled reluctantly. "I could never stay mad at you."

"Am I allowed to hug my commanding officer?" he asked with a smile.

She laughed and pulled him into a hug.

"Congratulations by the way," he said as they started walking again.

Kate shrugged. "It's no big deal."

Evan smiled. "Sure."

"Oh look, the infirmary, I get to abandon you," she said with a smile.

He gave her a childish push on the shoulder.

"You're coming out with us later, right?"

"When?"

She shrugged. "Sometime tonight, it's John's thing. He thinks we should blow off some steam before we go. But not too late, I have to be in early for briefings."

He nodded. "Sounds like fun. I assume I can crash at your place?"

She smiled. "Always."


	13. Marty

_Knock, knock._

Jack turned to see Colonel Sheppard standing in the doorway, looking uncomfortable.

"Come in Sheppard," he said.

"Thank you sir," said John, stepping into the room.

"Please, I'm retired, you can call me Jack."

John shifted awkwardly. "I don't think I'm quite ready to do that sir."

Jack smiled. "That's understandable. What can I do for you?"

"It's about Katie," John started.

"It's very admirable that you're worried about her, but she's the best person for the job, I'm not going to leave her behind."

John smiled slightly. "Why does everyone keep thinking I'm trying to get her left behind?"

"You're not?"

"No sir, I know how much this means to her; I just wanted to ask…"

Jack held up a hand. "Don't worry Sheppard, I'll watch out for her."

"Thank you sir."

"But Sheppard?" Jack said as John turned to leave. "I wouldn't let her know you're getting people to watch out for her. I know her a little, she's got your temper, and she wouldn't like you babying her."

"Yes sir."

"But that being said, I'll keep her out of trouble. She's kinda grown on me."

* * *

Kate stood outside General Landry's office, bouncing nervously. The General was in there with Captain James, briefing him on over a decade of confidential material. It had taken some convincing to get James on the team, and most of the resistance had been from him. He had finally come around after a personal visit from Kate, accompanied by Jack. She had convinced James that what he was being offered was an experience of a lifetime, and that, with the added weight of a formerly retired general being called back, had changed his mind. He had signed the confidentiality agreement, come to the SGC and was now being clued into what it was he had gotten himself into.

"Hey there," said a voice from behind her. She turned to see Daniel coming up the stairs from the control room.

She smiled. She had not seen Daniel much in the week or so since they had gotten there and she missed him. "Hello."

"Are you waiting to see General Landry?"

"No, I'm waiting for my friend; he's in there right now."

Daniel peeked past her through the window. "Ah, Captain James. Jack told me about him. He seems like a good kid."

Kate laughed.

"Did I say something funny?"

She shook her head. "It's just John also referred to him as a kid, and I can't help but think you're getting a bit old when you refer to a 27 year old as a 'kid.'"

Daniel smiled. "I suppose you're right, but still think he seems like a good…guy."

Kate laughed again. "Yes, he is. I've known him since back at the Academy. We used to cheat off of each other's homework."

"I never cheated."

Kate turned around with a smile to see James standing in Landry's doorway.

"I seem to remember _you_ cheating, but I never did." He stepped into the room and gave Kate a hug. "Hi Kitty," he said.

She hit him lightly on the arm. "I told you not to call me that." She caught Daniel's eye and smiled apologetically. "I'm sorry, Daniel Jackson this is Captain James. Marty, this is Dr. Jackson."

The guys exchanged pleasantries, shaking hands.

"I understand that Katie had to twist your arm pretty hard to get you on this mission," Daniel asked.

James nodded. "Yeah, but I'm glad that she did. After what General Landry's been telling me, I can't believe I almost said no."

"Yes, it is hard to resist."

"Well Marty, the rest of our team has arrived if you'd like to meet them?"

James nodded. "It was very nice to meet you Dr. Jackson."

"You too Captain James. I hope you enjoy your adventure." Daniel turned to enter Landry's office.

"Wait Daniel," said Kate. She turned and muttered something to James, who nodded and headed down the stairs. She turned back to Daniel. "Thank you very much for this."

"For what?"

"I know my brother asked you to get me on this mission, and I'm very thankful, to both of you."

Daniel smiled. "Katie, I didn't do anything. There was never any question about you being on this mission."

"Really?"

He nodded. "And in all honesty many people, myself included, felt that you were the best person to _lead_ this mission, but the IOA couldn't be talked into it."

Kate blushed. "That's very flattering, but I don't think I could handle all that responsibility. I'm just fine with my team."

"Well I'm glad."

"But still, thank you. Without you I never would have gotten the opportunity for any of this. I'd probably be teaching…English as a second language or something." She laughed. "So, thank you."

* * *

"This is quite a gig you've got here," said James as she came down the stairs into the control room.

Kate smiled, looking through the window at the Stargate beyond. "You seem to be handling this very well."

James laughed. "I anticipate freaking out the first time I step through there."

"It is a bit intimidating. My first time was only a few weeks ago."

He gaped at her. "Really?"

She nodded.

"Wow."

"Don't worry; the other members of our team are a little more experienced. Let's go see if we can't find them."

She led him down the stairs into the hallway.

"So a science geek and another military guy?"

"Yes. Major Lorne will be my second, sorry Marty."

He shrugged. "It's all right. He's higher ranked."

"And Dr. Radek Zelenka is our other team member. He was second in charge of the Atlantis science team and is one of the foremost experts on Ancient technology. He has some frustrating interpersonal skills, but most science nerds do."

James laughed. "You're a bit of a nerd yourself."

"That she is," said John, coming up behind them.

"Johnny," said Kate with a smile.

"Uh-oh, she's pulled out the pet name. I think I might be in trouble."

She hit him lightly. "Sometimes I'm allowed to like you."

"I guess."

"John, this is my friend Marty," she said, indicating James.

"Nice to meet you sir," said James.

"You too Captain. I've heard quite a bit about you in the past few weeks."

"I've heard quite a bit about you in the past few years sir. Katie thought the worst when she hadn't heard anything from you. I'm glad to see you're still alive."

"Me too, but it's been close."

"Johnny don't scare him."

John shrugged innocently.

"Have you seen Radek and Evan?" she asked, changing the subject.

John gave her an inquisitive look at the use of Lorne's first name, but didn't say anything. "They've been cleared by Lam. Major Lorne left the mountain and I believe Dr. Zelenka is with Rodney somewhere, probably bickering like little children. At least that's what he's supposed to be doing, working with Rodney, not bickering."

Kate smiled at the image. "Did you talk to Evan before he left?"

"Yeah, he's going to join us tonight. I told him where."

"Yay, I'm so excited."

John laughed. "But we can't party too hard. It would be a bad impression if you were hung over tomorrow."

Kate grimaced. "Briefings are bad enough without feeling like you're half dead."

"Yes. Well I've got to go see if I can spur the whiz kids along."

"What are they doing?"

"Messing with the ZPM that we got from Adrianus' lab."

"I thought you were going to keep that at Atlantis?"

He shrugged. "Well, we have one for now and something has to power this trip."

Kate smiled. "17 hundred hours right?"

John nodded.

"All right, I'll see you then."

He nodded again and continued walking down the hall.

"What's at 17 hundred?" asked James.

Kate smiled. "We're going to get our first look at our new home."


	14. Bold Decisions

"Dial it up," said Jack.

Walter nodded and started the dialing sequence. McKay and Zelenka had hooked up the ZPM and now everyone was waiting with baited breath as the chevrons locked. There was a collective intake of breath just after the seventh chevron locked. There was a heartbeat where it seemed that the eighth would not engage and then there was the telltale _swoosh_ of the forming event horizon and Walter's voice saying, "Chevron eight locked."

There was an increased air of tension as the MALP proceeded up the ramp and through the shimmery blue surface. They turned as one to the little screen showing nothing but snow. And then the static began to clear and they had their first glimpse of Praesidium. The gate room was larger than that of Atlantis and was lined with giant windows that gave a breathtaking view of space beyond. Kate was so wrapped up in what she was seeing that she almost missed how she was seeing it. The MALP was clearly floating in the weightlessness of space.

"Sir, we're not detecting any life signs," Carter was saying. "We're not detecting any atmosphere either. It appears that whatever was originally keeping space out is no longer working."

General Landry sighed. "All right, shut it down and we'll discuss our options."

Kate felt a little pang of sadness as the gate shut down and the MALP image disappeared. She caught Radek's eye as everyone began filing upstairs.

"Do you have any ideas?" she asked.

"I believe that it is just a matter of turning the gravity and atmosphere on. It looked much the same as Atlantis when we first got there, with everything powered down."

"And do you think you could power it back up?"

He shrugged. "That depends. Atlantis' ZPM was depleted but we were able to hook up our naquadah generators to their systems. If we can do the same—which we should be able to—then I don't see a problem. And that is assuming there's not a usable ZPM."

"That's what I want to hear. Now we just have to convince them," she pointed above them to where the briefing room was. "We should get up there."

When they got upstairs everyone else had already gotten settled.

"Well what do we do?" asked Daniel as Kate and Radek sat down.

"I don't know Dr. Jackson," said Landry. "The Daedalus is on its way back to Atlantis and the Apollo is still getting repairs."

"We don't need a ship," said Kate. "We can go through the gate."

"Were you not just in there?" asked John sarcastically.

"I have already discussed the situation with Dr. Zelenka and we've come to the conclusion that it is most likely just a lack of power. With a proper power source the systems can be brought back online."

"That's possible sir," said Sam. "It may just be that the Ancients shut things off when they left."

"Yes, and that's a good point to bring up. Why did the Ancients leave?" asked Cam.

"Well we won't know unless we go," said Kate determinedly.

"I appreciate your enthusiasm Dr. Sheppard," said General Landry, "but what happens if you can't bring the systems back online? You'll be stranded there."

"Not necessarily. The Daedalus is not quite to the Pegasus galaxy, correct?"

He nodded.

"Then have them divert their course a little. We go through and if we can't fix it, we gate to another planet and wait to be rescued. I am confident that even if we can't restore full power we can at least dial out to a nearby planet, and I even know which ones to try, thanks to Adrianus. I think this is too big an opportunity to continue to wait, especially considering the…reluctance the IOA have showed since making their initial decision. Any more delay and they might postpone it indefinitely."

Everyone around the table was staring at her slightly dumbfounded, except for Jack, who was looking at her with a quirk of a smile.

"She's right Hank. If we're gonna do this we need to do it now."

Landry considered for a moment. "Oh all right. But only your team Dr. Sheppard. If you get things up and running we'll send the rest."

Kate smiled. "Thank you sir."

"Thank me by finding a way to stop the Wraith. Now if you'll excuse me, I need to use my special red phone. I think the President would probably like to know what we're doing. We'll follow the original plan, you leave day after tomorrow."

* * *

"That was bold what you did in there," said Jack, catching Kate in the hallway.

Kate smiled. "Thanks. I kinda felt like I was channeling you actually."

Jack laughed. "It's possible. Look," he said, getting serious, "you should have gotten this command. If I had had any doubts before they would all be gone now. You should know that me being in charge is just temporary."

She nodded. "I understand, and in all honesty, I don't want to be in charge. I've seen how stressed you were when you were running this place, how stressed Landry's been, I don't want that. I'm fine with taking commands."

Jack looked at her skeptically.

"Oh all right, I'm fine with taking commands that I was going to do anyway."

Jack laughed. "You remind me more and more of your brother everyday."

"I'll take that as a compliment. Are you coming out with us tonight?"

Jack shook his head, looking past her to where Sam was walking down the hallway with Daniel. "I had thought about it," he said, looking back at Kate. "But I think I'm needed elsewhere."

Kate glanced over her shoulder and smiled. "That's good too, and that way at least one of us will be conscious tomorrow."

"You plan on being unconscious?"

"Semi, I don't hold my beer so well after 5 or 6."

Jack laughed. "Sounds like I'll be missing out."

"Not really."

"Hey," said John, coming up next to them. "You ready? It'll take us a bit to get there."

Kate nodded. "Last chance," she said to Jack with a smile.

Jack laughed. "I'll see you bright and early tomorrow."


	15. Of Love and Space Travel

The alarm clock went off shrilly, digging at the headache that was already raging full force in Kate's head—she had had _far_ too much to drink the night before. With a groan she shifted to turn off the sound, but another hand got there first, reaching over her. With a smile she rolled over to see Evan smiling at her.

"Good morning," she said.

"Is it?"

She laughed. "Well, maybe we did party too hard." She groaned. "I have a briefing in half an hour that I am _not_ looking forward to." She snuggled in closer to him. "Can't I just stay here with you? I like it here."

He laughed, wrapping his arms around her. "I think it would probably be best for us all if you knew what you were doing."

She sighed. "Oh all right." She got up from the bed and rummaged around for her clothes. She turned back to him, modeling her black fatigues. "Do you think anyone will notice that I'm wearing the same clothes as yesterday?"

Evan laughed. "I think you'll be ok."

Kate crawled across the bed and kissed him, then getting to her feet she grabbed her jacket and went out into the living room.

"Kat?"

She turned to see him standing in the doorway in his boxers, holding her duffel bag.

"You might need this."

She laughed, coming back over to him to get it, and another kiss. "All right, I'll see you later then?"

"Yes sir," he said with a mock salute.

She grabbed her bag from him and looked around to make sure she wasn't forgetting anything. "I really have to go don't I?"

"Go!" he said with a laugh.

She smiled, turning to open the door, but the person standing there wiped all mirth from her face.

"Major?" said John, looking past Kate.

With an awkward smile she pushed John back into the hallway. "Bye," she said to Evan apologetically before following her brother out.

"What the _hell_ was that?" he asked as soon as she had closed the door.

"I'm a big girl John."

"Damn it Katie, he's on your team. It's inappropriate."

"I know how to separate my work life from my personal life."

"It's not about that Katie. You're working for the military now. You could get in serious trouble for this."

"Well, I'm not _in_ the military John, so I don't see the problem. And we never got in trouble before."

They had arrived down on the street. John stopped dead, looking at Kate with a look she couldn't quite place.

"_Before_? What do you mean 'before'?"

Kate shifted uncomfortably. "I told you that I knew him back when he was at the SGC."

"Yes, but I didn't realize you meant in the biblical sense. Damn it Katie."

"Stop saying that, you're over-reacting."

"Does General O'Neill know about this?"

She smiled mischievously. "He's the one that introduced us."

John sighed. "Just…just get in the car; I don't even know what to say anymore."

Kate threw her bag in the bag seat and got in. "John it's not a big deal, ok. And I don't know why you're getting all worked up, it's not like you don't understand."

"I'm sorry?" he said as he started the car and pulled out.

"Oh please, I've seen the way you look at Elizabeth, are you telling me that there's nothing going on there?"

John was taken aback. "What do you…What are you…no, _no_, there's nothing going on."

She laughed. "That was a well constructed sentence, really. I know you Johnny; I know when you're in love."

"I am not…when did this become about me!? This is supposed to be about you sleeping with Major Lorne."

"You're not my dad John; I can make my own decisions."

"Well then make good ones Katherine. Getting involved with your team members complicates things. How can you focus on completing a mission when you're too focused on one of your team?"

"I don't see my connection with Evan as any different from my connection with the other guys." She paused. "Ok, maybe a little different. But watching Jack and Daniel and them, and watching you over the past few weeks, love is an important aspect of your team dynamic. You love all your team mates, even Rodney."

John was silent for a moment. "Do you love him Katie?"

She shrugged. "I don't know yet, do I have to?"

He sighed. "All right, we'll be done talking about this. But will you promise me something?"

"Maybe."

"Put the personal stuff on hold for a bit. This whole mission is complicated enough without you adding to it."

Kate sighed. "Fine. But can you promise me something?"

"Maybe."

"Tell Elizabeth how you feel."

John frowned. "I don't know what you mean."

Kate shot him a look but let it be, in the meantime she closed her eyes and rested her head on the cool window; she should have taken some aspirin.


	16. Andromeda

The following day and a half was a blur of preparations, briefings and endless medical procedures. Whenever Kate got a moment or two to herself John was close by, watching over her. She knew he was just anxious about her leaving, but things were stressed enough without his constant attention.

Finally the time came to depart. Kate's team and a science team assembled in the gate room with their gear and their space suits. Kate looked up to the control room where General Landry, Jack, John, Daniel, Rodney and Elizabeth were all standing looking anxious. She saw Landry nod to Walter and the gate began to dial. Kate exchanged a look with her brother before fastening her helmet firmly onto her suit.

"You're clear to depart," said Landry's voice over the intercom when the gate had connected. "Good luck."

Kate nodded and stepped forward. The shimmering blue surface was so foreboding this time. Who knew exactly what was on the other side? Was she leading them to their deaths? She took a deep breath; she had to be strong for her team.

"Here we go," she said.

She closed her eyes and stepped through. She felt herself come through the other side and engaged her gravity boots. She slowly opened her eyes and looked around. It was the most amazing thing she had ever seen, ten times the beauty and majesty of Atlantis. She heard the sound of the others coming through. She turned around to them. Zelenka and the other scientists were taking things off the cart and Lorne was supervising, but Kate's attention was drawn to James. She smiled at the look on his face.

"It has that effect," she said with a laugh, remembering her brother telling her that.

James took a deep breath, trying to speak.

With a laugh Kate tapped on her radio. "Command this is Praesidium, we're through."

"Best of luck Doctor," said Landry's voice. "You have 18 hours of oxygen, if we haven't heard from you before then we will dial in and divert the Daedalus to your position."

"Understood sir, Praesidium out."

The gate shut down and they were plunged into darkness. Kate switched on her light and saw the others doing the same. She looked around the embarkation room. Zelenka and the scientists had unloaded the equipment they would need and had moved to the command room to see if they couldn't get things up and running. Lorne was still overseeing everything and James was standing there, gazing around in wonder.

"Hey Marty," Kate said. "You feel up to a stroll?"

James nodded, still unable to speak.

She turned to Lorne. "Captain James and I are going to poke around. Let me know if the nerd herd gets anything working."

Lorne smiled. "Will do."

Kate took a quick look around at the options for exiting the embarkation room before she finally decided on a stairway that led down from the control room. Adrianus' memories told her that she would like what she found down there. James followed, still dumbstruck. As the stairs opened up into a hallway that Kate followed he seemed to find his voice.

"How do you know where you're going?" he asked.

Kate smiled. "You know that symbiote that I told you about?"

"The snake in your head?"

She nodded. "Well he left behind his memories and thoughts and things like that. I'm remembering what he knew of the layout of this place."

"That's gotta be disconcerting, remembering a place that you've never been."

She laughed. "You have no idea."

"And where do the memories tell you we're going."

Kate smiled. "You'll see."

They continued down the hallway until they came to a door. Kate waved her hand over the console, but nothing happened.

"Damn it," she said. "I didn't think about that."

"What?"

She gave him a look. "Think about it Marty."

"Oh right, the power."

She sighed. "I guess we could try to manually open it?"

James shrugged. "How does one do that exactly?"

Kate smiled. "I'm not exactly sure."

James opened his mouth to say something, but just then the lights in the hallway came on and they felt the artificial gravity engage.

"Kat?" came Lorne's voice over the intercom. "Zelenka fixed the power."

Kate laughed. "I noticed."

"He also found something that he wants you to see. He's the in control room, do you know where that is?"

Kate dug around in the memories for a second until she found it. "Yeah, I know where that is. But there's something I want to check out first. I'll meet you there in a few."

"Ok," he said. "Lorne out."

Kate shot James a mischievous look before swiping her hand over the console again. This time the door opened. They stepped in and the lights turned on to reveal a very large room, filled with what looked like space ships. Kate smiled as she walked up to one.

"What are those?" asked James in awe.

"These are puddle jumpers," she said. "There are similar ships on Atlantis."

James laughed.

"What?"

"It's just all sinking in. I'm in another galaxy on a space station that's god only knows how old, looking at space ships. My life's never going to be normal again, is it?"

Kate laughed. "Probably not. Come on, Radek's waiting."

They met Dr. Zelenka in the control room where he and the other scientists were flitting from console to console excitedly. They also weren't wearing their spacesuits, which was something Kate hadn't thought of. With the restoration of the power came the restoration of life support.

"So what's up?" she asked Radek, taking off her helmet.

"Well, we didn't need to hook up the naquadah generators."

"The city has a ZPM?"

He smiled, then indicated the center console, where she knew the ZPM resided in from the one in Atlantis. "We have 5."

"Five?" she gaped at him. "But there are only slots for three."

"Two are in storage."

"Wherever these Ancients disappeared to they left in a hurry," she said.

Zelenka shrugged. "I guess."

"Well, I suppose we should probably dial Earth?"

He smiled. "Already done."

"And?"

"They'll be sending the rest within the hour."

Kate smiled and turned to James. "Well, what do you say we go pick out our quarters before everyone else gets here?"


	17. A Terrifying Revelation

Kate was waiting in the embarkation room an hour later to meet Jack as he led the expedition through the gate.

"General O'Neill," she said, ignoring his frown at his temporarily reinstated title, "welcome to Praesidium."

Jack smiled. "These are some sweet digs," he said.

She laughed. "Yes they are sir. We have a team poking around, but we'd love some company."

He nodded. "Maybe we'll get unpacked first."

"Well your office is this way." She indicated a room beyond the command room, much like Elizabeth's in Atlantis.

He sighed. "I haven't had an office for awhile…I liked it that way."

Kate laughed. "Well as you yourself stated, you won't be here very long."

Jack smiled. "Dare to dream," he said before going off to his office.

Kate smiled as she watched him go. She was beginning to think she was_really_ going to like this mission. She continued to stand there as the other personnel trouped through. It gave her the chance to inspect the gate. She had noticed when she was in Pegasus the differences between those gates and the Milky Way gates. The Andromeda gate was equally unique. It was larger than the Pegasus gates, but smaller than the Milky Way ones. The constellations were the same as the Pegasus ones, though they lit up red as opposed to blue. She had just begun to count the symbols to see how many there were when something clicked in her head.

"Jack!" she yelled, abandoning her post by the gate and quickly rushing over to his office.

"What is it?" he asked, concerned, thinking something had gone wrong.

Kate smiled. "I remembered something."

Jack sighed. "Don't do that to me Sheppard, I thought we were being attacked or something."

"Sorry," she said sheepishly.

"All right, what did you remember?"

"A gate address, to a planet where the scientists were working on a way to stop the Wraith."

"But you still don't have any idea of what that is?"

Kate shook her head. "I'm still coming up empty. Maybe if I was there…?"

Jack smiled. "Oh all right. I suppose you'll be wanting to go now?"

She smiled.

"You just want to fly the puddle jumper, don't you?"

Kate laughed. "Is it that obvious?"

"Go. Get your team and go find out if there was a point to this mission."

Kate paused at the door. "You don't think it'll have been worth it even if we don't find a weapon against the Wraith?"

Jack looked around, past the windows to space beyond and smiled. "I guess exploration for exploration sake is ok."

She smiled. "What a concept."

* * *

"You're good to go," said Jack from the command room.

Kate and her team were waiting in the jumper bay in one of the ships. Radek had already had a thorough look around and approved. Evan had wanted to fly, but Kate beat him to it, promising that he could fly the return trip.

"Open the door Radek," she said.

Zelenka hit the button that opened the hatch above them and Kate eased the jumper up into the gate room.

"Here's hoping you find something," said Jack.

"Something useful," Kate amended.

"Yes, that."

Kate smiled as she guided the jumper through the gate. They came out the other side in space and followed the energy readings they were picking up down to the surface. As the cloud cover cleared they got a view of the planet, and it wasn't pretty.

"It looks like something bad happened here," said James, peering over Kate's shoulder through the window.

The surface of the planet was a wreck of old fallen buildings and other rubble. The air was thick with dust and smoke, as if the destruction had just happened, but based on the state of damage Kate guessed that it had happened a long time ago.

"I'm gonna put us down near the city there," said Kate, guiding the jumper what seemed to be the outskirts of the city. "All right I don't trust this place, we're sticking together," she said when they had landed and opened the rear hatch.

"I agree," said Evan, looking around warily.

They stepped out of the jumper and were immediately struck by the air. It was like walking into an oven of thick, pungent air. It was breathable, but just barely.

"We're gonna make this quick," Kate coughed.

The others nodded.

"Do you have any idea what happened here?" Radek asked her.

She shook her head. "Whatever it was had to have happened after Adrianus left, because I think that I would remember something like this. Maybe not at first, but definitely after being here, and I've got nothing. The last time he was here this place was whole."

They moved out, heading into the city in a tight little group.

"Are you getting anything Radek?" Lorne asked.

The Czech shook his head in bemusement. "I'm getting some strange residual energy signals, but it seems to be coming from everywhere."

"Whoa!" said James, swiveling around and bringing his gun up as if he had seen something.

"What is it?" asked Kate, turning in the direction he was looking.

"Something moved down there." They were looking down a side street. "It looked human."

"Hello?" Kate started to say, but only got out "Hel—" before a hand was over her mouth. She fought off Evan's hand and turned to face him. "What is going on?"

"We need to get out of here right now."

"Why?" She had never seen him look so terrified.

"Just trust me, I'll explain it all, but we need to go _now_."

She nodded. "All right."

They turned and headed back to the jumper, Lorne constantly increasing their pace. They were almost there when they heard it; a scuttling sound that Kate would have said was bugs if it didn't sound so metallic. She turned to look back but Evan grabbed her arm and pulled her forward. They were full out running by the time they reached the jumper, Lorne raced in and went right to the pilot's seat. The others had barely made it into the ship before he closed the hatch and took off. It was only then that Kate realized that Zelenka looked as freaked out as Lorne.

"What is going on?" she asked again as they shot into the air.

"Dial the gate," Lorne said, ignoring her question.

"Damn it Evan, what is going on?"

"Dial the gate and I'll tell you."

With a sigh she complied, she would yell at him later. "Now would you like to tell me what was so dangerous down there?" Kate asked when the wormhole was established.

"I should have noticed it right away from the energy readings," said Zelenka.

"I knew I had recognized the material those buildings were made out of, but it wasn't until Captain James said that he saw movement that it connected," said Lorne.

"What?"

"The only thing that would have survived in that atmosphere long term."

Things were starting to line up in Kate's head, but she couldn't believe that they were saying what she thought they were saying, and she said as much.

"I'm afraid so," said Zelenka.

Lorne shook his head miserably. "Replicators."


	18. A Turn for the Worse

"_Replicators_!?"

They had made it back to Praesidium in one piece and had just finished relating to Jack what they had seen. He was understandably upset.

"Yes sir," said Lorne.

"You're sure?" Jack asked.

"Unfortunately yes," said Kate.

Jack heaved a sigh and put his head in his hands. "This isn't good."

"No sir." Kate paused and took a deep breath. "What do you think we should do?"

"I would say that we should just ignore it and hope that they won't bother us, but I know that's not an option. I also know that going home isn't an option, so this is what we're going to do. Dr. Sheppard I'd like you and Dr. Zelenka to see what you can gather from the city's database, any information that would help us. Major Lorne I'd like you to take a team back to the replicator planet."

"Sir?"

"I assume that these jumpers have cloaks just like the others so you'll be there for recon only, see what you can find out."

"Yes sir."

"Here's hoping that these replicators are different than their Pegasus counterparts."

They all nodded their agreement.

"All right, let's move."

* * *

"We're under fire!" came James' voice frantically over the radio. 

"What's going on?" Kate asked as she rushed into the command room. "They just left."

"The Replicators detected them," said Jack.

Kate cursed under her breath. "How'd they do that?"

Jack shrugged. "Guess they are different than the Pegasus ones."

"Clearly." She glanced at the open gate. They had recently discovered the shield, and it was currently still activated. "Are they going to make it?"

Jack looked at her, but didn't say anything.

Kate turned back to the control console, as if the Ancient device held the answers. They waited for what felt like a lifetime before the technician said, "Receiving their IDC."

"Lower the shield," said Jack.

The jumper shot through the gate seconds later and the technician immediately shut down the wormhole. The floor retracted and the ship eased down into the jumper bay.

Jack and Kate exchanged a look before turning and proceeding down the steps that would lead them to the bay. Lorne and his team were just coming into the hall when they reached the bottom of the stairs.

"So that went well," said Lorne sarcastically as he came up to them.

"What the hell happened?" Jack asked.

"Well sir, we're not really sure."

Jack looked at him questioningly.

"Perhaps we should talk about this on your way to the infirmary?" Kate suggested.

The others nodded and the proceeded up the stairs.

"We had just descended into the atmosphere and everything seemed to be fine, and then out of nowhere we were surrounded by ships," Evan said as the walked through the halls. "They seemed to know exactly where we were, despite our cloak. I don't even know how we got out of there alive."

"Some damn good flying," contributed James. "The Major pulled off some nice moves and we managed to get away."

"Thank you James," Lorne said modestly.

"Yes sir."

"I don't know how they knew we were there," said Lorne, looking at Jack.

"I think that I might know."

They turned to see that Zelenka had joined them in their trek to the infirmary.

"I've just come from the archives and I've found some interesting information."

"Oh yeah," said Kate "I forgot that that's why I came up to the command center in the first place, to tell you what we'd found."

Zelenka nodded. "Well I found some more."

Kate gave him an inquisitive look.

"Perhaps you should start first Dr. Sheppard and then I will tell you what I have found."

Kate nodded and then turned back to General O'Neill. "We learned that the Ancients built the Replicators here to help them in their creation of a weapon against the Wraith. After the disaster that was the Pegasus Replicators the Ancients here, known as the Tanisians, moved their operations to another planet where they hoped that if the Replicators rebelled it could be contained. They continued their research, although we still can't find any reference to what it actually was, it's like all documentation of it has been wiped from the computer. That's all I've got." She turned to Zelenka.

"Well it appears that there eventually was a war between the Tanisians and the Replicators."

"Could have guessed that from the state of the planet," said Lorne.

"Yes well, what we couldn't tell is that the Replicators were the victors."

"What?" asked Jack and Kate in unison.

"Yes, it appears that the Replicators advanced at a rate that the Tanisians could never have predicted. They developed methods of detecting ships through their cloak. They managed to wipe out the Ancients entire fleet of warships. It was then and only then that the Tanisians decided to cut their loses and leave Praesidium. It is my belief that they wiped the computers of their research."

"But I thought you said that they created the Replicators to help them, wouldn't they know about the weapon then?" Lorne asked.

"They were created to be servants," said Kate, "not equals. They didn't know what they were helping with."

"But the Tanisians feared what they could do with that knowledge," said Zelenka. "So they got rid of it."

They had arrived at the infirmary by now.

"So then what happened?" asked Jack.

"They shut down the city and abandoned it. They believed that if they and the information were no longer here the Replicators would leave it alone and that they could someday come back with the help of their brethren in the Pegasus galaxy."

"That didn't work out too well," said James.

"No, it didn't. It is my belief that the Tanisians evacuated this city at roughly the same time as the Lanteans were evacuating Atlantis. When they all returned to Earth and realized there was nothing they could do to help each other they must have decided just to stay there and make lives for themselves."

"Well this leaves us in a difficult position," said Jack.

"How so sir?" asked Kate.

"We've just shown the Replicators that their most hated enemy is back in this city and they probably think that we have the knowledge that was taken out of the computer. They're not going to stop until they have it."

"So what are you saying sir?" asked Kate, though she was pretty sure she knew where this was going.

"I'm saying we need to pack up and get the hell out of here. We leave no trace that we were here therefore giving them nothing to trace us back to Earth with."

Kate and Lorne stared at him, dumbstruck. "I can't believe you, the great Jack O'Neill of all people, are saying that we need to turn tail and run," Kate said.

"Sometimes that's the best course of action," he said unconvincingly.

Kate shot him a look.

"Look if it was just me and you Kate I'd be all for nuking the bastards. I hate Replicators; I don't think anyone hates them quite as much as I do. However, it's not just you and me. We have a whole city full of people to answer to, and a planet full beyond that. It's my duty to make sure that they're safe."

Kate sighed, but anything that she had been about to say was cut off by a frantic call on the radio that changed everything.

"General O'Neill……under attack….lost jumper bay….."

The message ended in screams and then static.

They all looked at each other, the unspoken hanging on the air. The Replicators were in the city.


	19. Repercussions

_Just a quick note: if you've not read my story "Generations" then there are a few things that might be (and may have already been) confusing. especially the part about Sam's son. my advice would be just to go and read the story (also cause i want people to read it and give me feedback)  
_

* * *

John had just settled back into his room after coming back from Earth when there was a call at his door. 

"Come in," he said, getting up off the bed.

The door opened and Elizabeth stepped in.

"Elizabeth," he said somewhat awkwardly. He hadn't really spoken to her since before Kate had left. Mostly because he knew his sister was right. His feelings for Elizabeth were more than they should be and he didn't know what to do about it. "What's up?"

"John we need to go back to Earth."

"Now?"

"Yes, they just radioed through the Daedalus. Something's happened."

John suddenly felt icy cold. "Something's happened where?"

She shook her head. "I wasn't given any details, they just told us to come."

John nodded; dazed, only capable of thinking that is was a good thing he hadn't unpacked. He grabbed his duffel and followed Elizabeth out of the room. They met Rodney in the gate room and the three of them waited in silence as Chuck dialed the gate. The gate activated and they stepped forward.

The scene on the other side was not at all what John was expecting. Wounded people were being carted off to the infirmary, some of the stretchers were covered in a blanket and John knew were they were going. They looked over to see General Landry wading through the chaos of the room to meet them.

"Colonel Sheppard, Dr. Weir, Dr. McKay, if you'd please follow me."

"What happened sir?" John asked.

"If you'll follow me we'll discuss it in the briefing room."

He turned to lead them out but just then John spotted the weapons the marines were holding.

"Sir, why do those men have ARG's?"

Landry looked back at them. "I promise I will explain everything to the best of my ability. Unfortunately I still do not know all the details myself. We'll be skipping your post gate travel examinations for the sake of time."

John was going to say something else but Elizabeth cut him off.

"Lead the way General."

Landry nodded and led them into the hallway. Elizabeth shot John a warning look before following the General.

"Walter," said Landry as the walked through the control room.

"Yes sir?"

"Is everything set up?"

"Yes sir."

"Very well. Call me if anything happens."

"Yes sir."

Landry led them up the stairs and into the briefing room. "Please have a seat."

The three of them sat down and turned their chairs to look at Landry.

"Sir, will you please tell us what's going on?" asked John.

Landry sighed. "Roughly 40 minutes ago the Andromeda team dialed in. They were under attack."

John flinched, but managed to keep his thoughts to himself.

"This was the message." Landry picked up a remote and pressed a button, they immediately heard Kate's voice over the speakers.

"_Command this is Dr. Sheppard, we are under attack and request an immediate evacuation. We ask that you open the iris and allow us to start sending through personnel beginning with our casualties and…fatalities."_

"_Dr. Sheppard, who is attacking you?" said Walter._

"_We are under attack from beings similar to…to the Replicators."_

John and Elizabeth exchanged a frantic look. _Replicators_?

"_Suggest military personnel equip themselves with ARG's, we can't guarantee that some won't slip through," said Kate._

"_You are cleared to start sending through your wounded."_

"_Thank you."_

The recording ended.

"_Replicators_?" Rodney asked in disbelief.

"I am afraid so Dr. McKay."

"There's more to this," said Elizabeth, "otherwise you wouldn't have brought all three of us back."

"Where's my sister?" John asked.

Elizabeth gave him another look, but he ignored it.

"Sir, where's my sister?" he demanded.

"The Andromeda team began sending their wounded through almost immediately and for nearly 15 minutes it seemed that they would be able to get everyone out. They had just begun to send non-injured personnel through when we first lost the radio signal and then the wormhole shut down."

John was dumbstruck. Landry had pretty much just told him that his sister was dead.

"Are you saying that the rest of them are lost?" Elizabeth asked.

"We're not entirely sure of much. As you could hear we weren't given much to go on, and a lot of the injured are in shock and can't tell us much of anything. We haven't given up on those that are still there. We're waiting 24 hours to see if we hear anything before we decide what action to take."

"24 hours sir? What good will that do?" John's tone was bordering on insubordination.

"John," Elizabeth hissed.

"If you'll come with me we can head down to the infirmary and see if we can't get some more answers together," said Landry, ignoring John's question.

John grudgingly obliged. As he stood up he felt a hand slip into his and turned to look into Elizabeth's face. Her eyes were full of comfort and compassion and John couldn't help but feel that everything was going to be all right somehow.

* * *

The first thing they saw upon entering the infirmary, after the bustle that was going on around them, was the small group of people clustered around a bed at the far end of the row. Daniel turned and walked over to meet them, leaving Sam and an unfamiliar boy leaning over the still figure in the bed. 

"Hi there," he said timidly.

John looked past the archaeologist to the figure in the bed. It was General O'Neill.

"What the hell happened?" he asked.

Daniel looked over his shoulder, then back at Sheppard. "We don't exactly know. From what we've been able to gather from Jack—when he's lucid—and some of the others the Replicators snuck in on one of the jumpers. Once in they completely took over the jumper bay. Jack was injured as they fought to keep the gate room. It is my understanding that your sister then took command and dialed Earth to get everyone out of there. What we've heard from the last few people through the gate is that they were losing the gate room. We don't know what happened after that."

"We know, we've heard the recording," said Elizabeth.

They turned to see that Sam had left Jack's side and come over to them. John could see the tear tracks down her cheeks and was reminded that he wasn't the only one here who could lose someone they loved.

"Sam I—" he started, but didn't know what to say. He wanted to hug her, but didn't know if it would be appropriate.

To everyone's surprise Rodney stepped forward and enveloped her in his arms, and even more surprising, she hugged him back.

"It'll be ok," he said to her as he pulled away.

She gave him a weak smile. "I know. He's pretty tough. I'm sorry you came all the way down here for nothing," she said, apologizing for Jack's unconsciousness. "He's been out for awhile."

"It's all right," said Elizabeth. "We understand."

"He's going to make it," said Daniel. "Dr. Lam is confident in that."

"That's good."

"John I'm so sorry about Kate," said Sam. "I have complete faith that she's ok."

"Thank you," he said with a weak smile, though he didn't really mean it.

"Well, since Jack is still unable to give us any details, perhaps we should adjourn this little meeting," said Landry. "I'm sure there are places you'd all rather be."

Sam glanced back at the bed, and the boy beside it. "General if it's not too much trouble I think Jake and I will be staying on the base."

Landry nodded his understanding. "I'll have Walter take care of that."

"Thank you sir. If you all will excuse me?" She went back over to the bed and put her arms around the boy.

John just had to ask. "Who's that boy?"

Daniel glanced back at them and smiled. "That's Jacob, he's Jack and Sam's son."

"What?"

Daniel shook his head. "It's a long story."

John shrugged; he had to do something to keep his mind off things. "I've got time, wanna get some coffee?"

Daniel nodded and the four of them left the infirmary, leaving behind, if only for the moment, the reminder that all was not well.


	20. Choices

"They've completely taken over the command room," said Lorne. "There are human forms everywhere."

Kate swore under her breath. "Have they figured out what we did to the control room?"

Zelenka shook his head. "They still have been unable to restore power."

Kate nodded. It had now been nearly a day since the Replicators had taken over the city. Shortly after they had taken the gate room Kate and her team had been able to sabotage the control room, disabling power from all but essential systems. This also meant that the Replicators had been unable to detect them. So far Kate and her team were the only survivors, but they had no idea if there were others out there in the city.

"What's our progress on dialing home?" she asked Radek.

He sighed. "We can do it, but not for long."

"How long is not for long?"

"One minute, maybe two."

"That'll be fine. We only need to contact the SGC and let them know we're still alive."

"What are we going to tell them?" asked James.

They all looked at each other, because they knew the answer, and it wasn't pleasant.

Finally Kate sighed. "We tell them that we're alive but we can't get to the gate because of a foothold situation. We give us 72-hours to try to retake the city. If by that point we haven't…we make sure they can't find Earth."

"Why can't they send a rescue?" asked James.

"It would take the Daedalus, Apollo and Odyssey combined to even put a dent in the Replicator's forces," said Lorne. "And even then we would probably sustain heavy loses."

"So there's really no choice then is there?"

Kate shook her head. "Either we get back the city, or no one gets it."

* * *

"Incoming wormhole!"

John was the first to Walter's side, followed closely by Elizabeth, Rodney, Daniel, Landry, and incredibly enough Jack, being supported by Sam.

"Receiving a message."

"SGC, this is Praesidium," said Kate's voice.

John let out a breath that he hadn't known he was holding. He felt Elizabeth's hand slip into his and gave it a little squeeze.

"We read you Dr. Sheppard."

"The city is swarming with Replicators; we've lost the gate room and are currently dialing from one of the city's sublevels. We were able to cut power to all nonessential systems and have since been evading capture."

"What are their numbers?" asked Landry.

"It's difficult to say, but there are a lot." There was a pause. "We are attempting to win back the city, but we do not know how successful we will be. We request 72 hours to try before counter measures are taken."

Landry and Jack exchanged a look and Jack nodded.

"Very well," said Landry. "In the meantime we will divert the Daedalus to your position—"

"No sir," she said. "That would not be wise. There are many Replicator ships around the city; I don't think she could take them."

Landry sighed. "Very well."

"Sir, Zelenka tells me that we don't have much time left. Is General O'Neill all right?"

"I'll live," said Jack.

Kate sighed in relief. "That's good to hear sir."

Jack smiled, even though she couldn't see it. "I'm glad to hear that you're ok too, make sure to stay that way."

"Yes sir."

They heard Lorne's voice. "Kat we've gotta go, they've detected us."

"We'll contact you in 72 hours if not before," said Kate, "Praesidium out."

The gate shut down and the group was left in silence. John was the first one to speak.

"Counter measures?"

Jack sighed. "We were given orders that if a situation like this arose the wrong information was not to be allowed into enemy hands."

"You've got to be kidding me."

"I'm afraid not son," said Landry.

"Well that's a load of shit."

"John!" Elizabeth said sternly.

He ignored her, pulling his hand away from hers and stepping toward Jack.

"General this is my sister we're talking about!"

"I know that John. There are a lot of people's sisters and brothers on this mission. It isn't just your family that's at stake."

"Damn it!" John started, but Landry cut him off.

"Colonel! You are getting dangerously close to insubordination for the second time in two days. Now I think we all need a break and we can come back to this in the morning."

"That sounds like a good idea sir," said Elizabeth, trying to ease the tension of the situation. "Come on John, I'll walk you back to your room."

John looked from her to Jack and back before reluctantly nodding. He followed Elizabeth out of the control room and out into the hallway. She took his hand in hers and led him back to his room.

"John you've got to keep it together," she said when she had closed the door behind them. "I need you in Atlantis; I can't have you sitting around here with a court-martial."

John sank onto the bed and put his head in his hands. "She's not going to make it back is she?"

Elizabeth sat down next to him and slipped her arm through his. "She's going to be all right John, I promise."

"How can you be sure?" he asked, sitting up.

"Because," she said as she leaned her head on his shoulder. "She's too much like you not to be."

John smiled weakly. "I should have been there before this."

"John," she sighed. "You have to stop beating yourself up over that. You did what you could."

John shook his head. "No, I didn't. Kate was right, I was a pushover. I should have told Paul to go to hell, that I was going to see my sister no matter what, and I didn't. Because I thought he was right. I thought that she would be better off if I disconnected from her. So I stopped talking to her and moved to Antarctica. She had every right to be upset with me, and now I'm never going to get to apologize."

Elizabeth sat back up and turned to look him in the face.

"I have complete faith in Kate, Radek, and Lorne's ability to fight back. But I also know that General O'Neill isn't going to be so quick to give up on them. So don't you worry, everything will be just fine."

As John sat there, looking into her eyes he thought of what Kate had said, and the fact that he had done nothing about it. And now with all this, he remembered how lost he had been when Elizabeth was taken, and how he had done nothing to show his feeling when they got her back. And here was his chance, the [perfect moment, and yet he couldn't seem to find the courage, and that thought made him laugh.

"What is it?" she asked.

"It's nothing," he said, turning away and trying to hider the emotion that was undoubtedly all over his face.

Elizabeth reached out her hand and slowly tilted his face back towards hers. Then she leaned in and gently kissed him, an act of comfort more than anything. But though it started out that way it was not destined to end that way.

John leaned into the kiss, wrapping his arms around her. She moved into the embrace as well, digging her hands into his hair and opening her mouth to him.

He pulled away after a moment. "Wait, wait, wait," he said. "What are we doing?"

"Something we should have done a long time ago."

John shrugged. "Just so we're clear."

Elizabeth smiled. "Crystal," she said before pulling him back in for a kiss.

* * *

_sorry for the shipping, i just had to get it in there cause i'm a die-hard John/Elizabeth fan and i felt that it needed to be there a bit, especially with the stuff that Kate said to him. so there, i'm done, it's out of the way._

* * *


	21. Deceptions

Kate hit the floor with a force that made her bones shake. She felt arms help her into a sitting position and leaned back into Lorne's embrace. She wiped the blood from her mouth and looked up at the person who had just thrown her into the cell.

Caynus looked down at the small group huddled in the corner and scowled. "You may think that you will be able to resist me forever, but you won't," she said. "I will return for you later." And with that she turned on her heel and left the brig, her skirt swishing around her as she left.

"Are you all right?" Evan asked.

She nodded. "I'll be fine."

"What did they do?" Radek asked.

"What we expected."

"Fingers in the brain?" James asked.

Kate nodded. "I think I did an ok job resisting them. We've gotta hope that I did. If they find out about home before the SGC can deliver its payload, we're in serious trouble." She sat up and scooted a little away from Evan, trying to support herself.

"You really think they're going to nuke this place?" James asked.

Kate nodded. "Yeah I do. Look Marty, you and I weren't there when the Replicators terrorized not only our galaxy but the Asgard galaxy and then later the Pegasus galaxy. We don't know what it was like, we only read about it. But Evan and Radek here lived through some of that and I'm sure they'll tell you that it wasn't a nice time."

They were both shaking their heads.

"The SGC can't afford to have this as a problem again; they'll take care of it by any means necessary."

"So what you're saying is either we break out of here or we're toast?"

Kate smiled at James. "I'm leaning more towards toast, but you go ahead and stay optimistic, it's refreshing."

She kneaded her forehead with her knuckles, trying to relieve the headache that was blossoming there. As she massaged her head the world seemed to flicker and she froze.

"Kat are you ok?" Evan asked, moving closer to her.

She shook her head to clear it, then nodded. "Yeah, just a little disoriented."

"Understandably," said Radek.

"Any thoughts on _how_ to get out of here?" James asked after several silent moments.

They all turned to look at Zelenka.

"Why are you looking at me?" he asked.

"Oh please," said Lorne. "You science nerds are always getting us out of tight situations."

"No, McKay is always getting us out of these situations."

"Well McKay's not here is he? So it looks like it's up to you. These prisons are just like the ones back on Atlantis."

Zelenka grumbled under his breath about McKay. "Look," he said out loud, "even if I knew how to break out of the Atlantis prisons, these _are_ different. I don't know if I can get us out of here."

Kate opened her mouth to say something when the door to the brig opened and a woman stepped in.

"Hello," she said with a smile. "My name is Jaina."

Kate recognized her from her interrogation. "She's a replicator," she said to the others.

Jaina smiled. "That I am, but I am not like Caynus. I believe that there are higher goals than domination."

"You're one of _those_," said Evan.

"I assume you are referring to our brethren in the Pegasus galaxy."

Lorne nodded.

"Yes, we are of the same belief, we aim for ascension."

"What does that have to do with us?" Kate asked.

"They believe that we are the key to them figuring out how to ascend," said Evan. "But it won't work. It never worked for the Pegasus replicators."

Jaina smiled. "But we are different from our brethren." She pulled a knife from her belt, rolled her sleeve up and put the knife to her skin. She dragged the blade across her skin and it blossomed red. They watched as the skin reknit itself and Jaina looked back at them. "As you can see we have evolved."

The group gaped at her.

"We encountered something like this in Pegasus," Radek said. "A small population was trying to advance, they created a duplicate of Colonel Sheppard's team, and they were much like you are. But that faction was destroyed by the others."

"Here in Andromeda we have advanced as a race, _all_ of us."

"I'm sorry, but why are you telling us this?" Kate asked.

"Because I want you to trust me."

"But why?"

Jaina waved her hand in front of the cell door, which opened. "That is why."

They got to their feet, Evan offering a steadying hand to Kate.

"You're letting us go?" she asked the Replicator.

Jaina nodded.

"What's the catch?" Evan asked.

"Catch? There is no catch. Several of us believe that as ensouled beings, capable of ascension, you should not be kept like this."

"So that's it? You're letting us go? How are we supposed to get out when we can't get to the gate room?" Kate asked.

"You do not need the gate."

Kate was confused, and was about to say so, when she was hit with a sudden flash of pain in her head that threw her back into Evan's arms. The world shifted again, and she could almost swear she was somewhere else, but then the world righted itself and she was back in the brig being embraced by Lorne. He was saying her name, with an urgency that suggested he had already been saying it for awhile.

"Katherine," he said.

"I'm fine," she said, pushing herself up to her feet. "You were about to tell us why we don't need the gate room," she said, turning to Jaina.

The Replicator nodded. "Several of my followers have maneuvered to be stationed in the south bay where one of our smaller vessels is docked. You will be able to commandeer it. It may be small but it does have a hyper drive and will get you to your home." There seemed to be a lingering question after her statement.

"We're not going to tell you where we're from," said Kate.

"I understand."

"Good."

Jaina smiled. "Then if you will follow me?"

They followed the Replicator woman out into the hallway. She led them along a convoluted path to avoid the sentries posted all over the city. They finally made it to the docking bay and onto the vessel.

"Won't you get into trouble for this?" Kate asked Jaina.

Jaina smiled. "Most likely, but I am willing to risk Caynus' wrath. Go home, and do not return here.

Kate nodded, and the world shifted a little again. This time she could swear she heard a voice say, "This one is strong."

"Did you hear that?" she asked Jaina.

The Replicator woman shook her head. "I did not hear anything, but perhaps you should not linger any longer."

Kate nodded again. "Thank you."

Jaina inclined her head. "You are welcome," she said before turning and exiting the vessel.

Kate closed the door behind the Replicator and made her way up to the bridge.

"Do you know how to work this thing Radek?" she asked.

"It's very similar to the Aurora-class vessels, only smaller."

"Does that mean that you know how to work it?"

He nodded.

"Then get us the hell out of here."

He and Lorne complied and soon the ship was away from Praesidium and heading into hyper space.

"As soon as we're close enough to the edge of the galaxy start radioing the Daedalus. They should be stationed between the galaxies."

Kate sunk into the captain's chair and put her head in her hands. It was still throbbing away.

"Kate, you should go lie down," said James.

She sat up and looked at him.

"We'll call you when we get through to the Daedalus."

Kate was reluctant, but another sharp flash of pain had her agreeing. She stumbled off the bridge and soon found some living quarters. She barely managed to make it to the bed before she passed out from exhaustion. She had terrifying dreams and woke up in a sweat. She tried to remember the dreams but couldn't, only the fear. There was a tap on her door and Evan entered.

"We were able to contact the Daedalus and we're on our way to rendezvous with them."

Kate sat up. "How long was I out?"

"Only a few hours. This ship has _very_ long range communication, and the Daedalus was a lot closer than we thought."

"How long before we rendezvous?"

"8 hours or so. James found the commissary if you're hungry."

"These things eat?"

He shrugged. "Apparently."

Kate sighed and ran her fingers through her hair. "I think I'll go to the control room and see what I can't learn about our friends."

Evan nodded. "All right. I'm going back to the bridge."

He left her sitting in the dark, feeling that something was wrong, but not quite able to put her finger on it. She got to her feet and the room lurched. She fell to the floor from the pain in her head. It passed once again and she was left panting on the floor.

"What the _hell_ is going on?" she asked to now one in particular.

She got to her feet and waited a moment to see if the world would shift again. When everything stayed as it should she made her way to the door and out into the hallway. She stumbled around aimlessly before she finally found the control room. She went inside and went straight to one of the computers.

"Well this doesn't make any sense," she said, looking at the display screen. "It's all gibberish."

The room lurched and pain blossomed again in her head.

"Kat?" came a voice from behind her.

She turned to see Evan standing in the doorway looking concerned.

"When did you get here?" she asked.

"Only a minute ago, but we tried radioing you and you didn't answer."

"I just got down here," she said.

"Kat, you've been down here for almost 8 hours."

Kate looked down at her watch. Sure enough 8 hours had passed.

"I must have…fallen asleep," she said.

He was still looking at her in concern. "We've rendezvoused with the Daedalus," he said. "We should be docked by now."

"Wow, I really was out for awhile."

Evan smiled. "Colonel Caldwell is waiting for us."

"Right," Kate said, glancing back at the computer display. "Lead the way."

They met up with the others on the way.

"Are you all right Kate?" asked Radek.

Kate nodded. "I'll be fine once we get back to Earth."

The world lurched again, more violently than before. She fell to the floor and rubbed her head, feeling that it would burst. The pain kept building and she suddenly knew what was wrong, what had been wrong all along. She began to fight against the pain in her head and her surroundings changed.

She was back in the brig of Praesidium, on her knees in front of Caynus, who had her fingers in Kate's head. The Replicator removed her hand, pulling with it a scream from Kate. Without the steadying force of Caynus, Kate fell backwards. Strong arms caught her before she it the floor. Evan pulled her close and cradled her in his arms.

Caynus laughed. "Your race is pathetic. _You_ are the ones more prized over us? I will enjoy wiping you from this plane of existence." She turned on her heel and left the brig.

"Kat," said Evan softly, pulling her even closer. "Katherine, please."

Kate didn't respond.

"She's in shock," said Radek.

"This is bad," said James. "We need to know what they showed her."

"He's right Lorne," said Zelenka. "They may know about home, they may know how to get there."

"It won't matter soon."

"I hope you're right," said Radek. "I sure hope you're right."


	22. New Beginnings

John rolled over and looked at the sleeping figure lying next to him. He smiled as he watched her breathing. Elizabeth was so beautiful, she always had been. He kissed her lightly on the cheek, but not waking her. He loved her more than he ever thought possible. From the first moment he had met her he felt some kind of connection. It had only taken a few weeks for him to know he loved her. He could pinpoint the exact moment. It had been as he lay in the jumper, stuck in the Stargate, dying from the Iratus bug latched to his neck. The thought of never seeing Elizabeth again had cut at him. He had almost told her how he felt, convinced that he would never get another chance. But he had survived, had gotten many more chances, and yet had never told her until last night. People had often thought that there was something between him and Teyla, but it had always been Elizabeth. Sure he loved Teyla, but rather the way one loves a sister. Elizabeth was his everything, and it turned out she loved him too.

"Stop doing that," she said, rolling over with a smile.

"Doing what?" John asked innocently.

"Staring."

He leaned in and kissed her. "I can't help it."

Elizabeth laughed. She moved in to kiss him when there was a knock on the door.

"Hold that thought," said John. He got out of the bed, pulled his pants on and made his way over to the door. He opened the door just a crack to reveal Rodney.

"McKay," he said.

"Morning," said Rodney. "General O'Neill wants to see us in the briefing room."

"All right, just give me a second."

"K. Hey, wait. Do you know where Elizabeth is? She's not in her room and the General wants to see her too."

John gave a small smile and opened the door the rest of the way.

"Morning Rodney," said Elizabeth from beneath the blankets.

McKay gaped at them, speechless.

John laughed. "We'll see you in a few McKay," he said. As he shut the door he could hear Rodney mutter, "Kirk."

* * *

"Hello there," said Jack somewhat cheerfully as they entered the briefing room.

"Sir?" John was confused.

"Have a seat."

John, Elizabeth, and Rodney sat down across from Jack, Sam and the rest of SG-1.

"We're reaching the 36-hour mark," Sam said. "They have another day and a half before we're technically supposed to send a bomb."

"Technically?" Rodney asked.

Jack nodded. "They would have contacted us by now if they were capable of it. Now we're not writing them off, just the opposite. We think that it's likely they've been taken captive and need rescuing."

John sat up a little straighter. "Sir, are you saying what I think you're saying?"

Jack nodded. "The Odyssey and the Apollo have been outfitted with Anti-Replicator weapons and had the ZPM's we salvaged installed. Colonel Sheppard, you and your team will be on the Apollo, SG-1 on the Odyssey. The Daedalus will rendezvous with you en route. Your job is to rescue our people and kick as much Replicator ass as possible.

"And the city?" Elizabeth asked. "Are you still going to destroy it?"

Jack looked at Sam, turning the answer over to her.

"Not if Rodney can give us another option," she said.

"Excuse me?" McKay asked.

"You found a way to defeat the Pegasus Replicators."

"That was a one-time deal! I don't have what I need to do that again. And besides, it would destroy the city."

"I have complete faith in your ability to reconcile those two things," said Jack. "You leave for Area 51, oh, now."

"Area 51!?" McKay asked as two marines entered to escort him out.

"Bye Rodney," said John with a smile.

"He'll figure something out," said Elizabeth confidently.

"Just throw a lemon into the mix and he'll have something in an hour," said John.

"You all leave in an hour," said Jack, bringing the conversation back to the serious. "The rest of your team has been contacted and will be here shortly." Jack stood up—somewhat unsteadily—and the others rose too. "Take back our people, take back the city. I don't need to tell you what will happen if you don't."

"Yes sir," they all said.

Jack leaned over and whispered something to Sam, who nodded. "Now if you'll excuse me," he said. "I have a date with Dr. Lam."

Sam helped him out of the room, leaving the others standing there in the tension. This was a very personal mission for most of them. Slowly they broke off and went their separate ways to prepare.

Elizabeth caught up with John in the hallway and sipped her hand into his. "I'm coming too," she said. "I know I'm not technically part of your team, but I want to be there."

John stopped walking and turned to her, taking her by the hands. "Are you sure that's safe? I mean after all you've been through?"

She shrugged. "I want to be there for you, for your sister, for Radek and Lorne. And who knows, I might be able to help."

John touched her cheek, cupping her face in his hand. He smiled at her. "Ok," he said, nodding.

Elizabeth glanced up and down the hall before leaning up and kissing him lightly.

John smiled at her as she pulled away. "What was that for?"

She shrugged. "For awhile."

He laughed. "I can live with that."

The offworld activation alarm went off.

"Looks like our friends are here," he said. "What do you say we go greet them?"

Elizabeth slipped her hand back into his and they proceeded down the hallway.


End file.
